Combinatorics and topological weights of chromatin loop networks.

Polymer physics models suggest that chromatin spontaneously folds into loop networks with transcription units (TUs), such as enhancers and promoters, as anchors. Here we use combinatoric arguments to enumerate the emergent chromatin loop networks, both in the case where TUs are labeled and where they are unlabeled. We then combine these mathematical results with those of computer simulations aimed at finding the inter-TU energy required to form a target loop network. We show that different topologies are vastly different in terms of both their combinatorial weight and energy of formation. We explain the latter result qualitatively by computing the topological weight of a given network-i.e., its partition function in statistical mechanics language-in the approximation where excluded volume interactions are neglected. Our results show that networks featuring local loops are statistically more likely with respect to networks including more nonlocal contacts. We suggest our classification of loop networks, together with our estimate of the combinatorial and topological weight of each network, will be relevant to catalog three-dimensional structures of chromatin fibers around eukaryotic genes, and to estimate their relative frequency in both simulations and experiments.

Fulvenallenyl Radical (C7H5·)-Mediated Gas-Phase Synthesis of Bicyclic Aromatic C10H8 Isomers: Can Fulvenallenyl Efficiently React with Closed-Shell Hydrocarbons?

To understand the reactivity of resonantly stabilized radicals, often found in relevant concentrations in gaseous environments, it is important to determine their main reaction pathways. Here, it is investigated whether the fulvenallenyl radical (C7H5·) reacts preferentially with closed-shell molecules or radicals. Electronic structure calculations on the C10H9 potential energy surface accessed by the reactions of C7H5· with methylacetylene (CH3CCH) and allene (H2CCCH2) were combined with RRKM-ME calculations of temperature- and pressure-dependent rate constants using the automated EStokTP software suite and kinetic modeling to assess the reactivity of C7H5· with closed-shell unsaturated hydrocarbons. Experimentally, the reactions were attempted in a chemical microreactor heated to 998 ± 10 K by preparing fulvenallenyl radicals via pyrolysis of trichloromethylbenzene (C7H5Cl3) and seeding the radicals in methylacetylene or allene carrier gas, with product identification by means of photoionization mass spectrometry. The measured photoionization efficiency curve of m/z = 128 was assigned to a linear combination of the reference curves of two C10H8 isomers, azulene (minor) and naphthalene (major), presumably resulting from the C7H5· plus C3H4 reactions. However, the calculations demonstrated that these reactions are too slow, and kinetic modeling of processes in the reactor allowed us to conclude that the observation of naphthalene and azulene is due to the C7H5· plus C3H3· reaction, where propargyl is produced by direct hydrogen atom abstraction by chlorine (Cl) atoms from allene or methylacetylene and Cl stem from the pyrolysis of C7H5Cl3. Modeling results under the copyrolysis conditions of toluene and methylacetylene in high-temperature shock tube experiments confirmed the prevalence of the fulvenallenyl reaction with propargyl over its reactions with C3H4 even when the concentrations of allene and methylacetylene largely exceed that of propargyl. Overall, the reactions of fulvenallenyl with both allene and methylacetylene were found to be noncompetitive in the formation of naphthalene and azulene thus attesting the inefficiency of the fulvenallenyl radical reactions with the prototype closed-shell hydrocarbon species. In the meantime, the new reaction pathways revealed, including H-assisted isomerizations between C10H8 isomers and decomposition reactions of various C10H9 isomers, emerge as relevant and are recommended for inclusion in combustion kinetic models for naphthalene formation.

Topological Spectra and Entropy of Chromatin Loop Networks.

The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fiber is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors and RNA polymerases. This physical model leads to the natural emergence of clusters of proteins and binding sites, accompanied by the folding of chromatin into a set of topologies, each associated with a different network of loops. Here, we combine numerics and analytics to first classify these networks and then find their relative importance or statistical weight, when the properties of the underlying polymer are those relevant to chromatin. Unlike polymer networks previously studied, our chromatin networks have finite average distances between successive binding sites, and this leads to giant differences between the weights of topologies with the same number of edges and nodes but different wiring. These weights strongly favor rosettelike structures with a local cloud of loops with respect to more complicated nonlocal topologies. Our results suggest that genes should overwhelmingly fold into a small fraction of all possible 3D topologies, which can be robustly characterized by the framework we propose here.

Specifics of Porous Polymer and Xenogeneic Matrices and of Bone Tissue Regeneration Related to Their Implantation into an Experimental Rabbit Defect.

This paper provides a study of two bone substitutes: a hybrid porous polymer and an osteoplastic matrix based on a bovine-derived xenograft. Both materials are porous, but their pore characteristics are different. The osteoplastic matrix has pores of 300-600 µm and the hybrid polymer has smaller pores, generally of 6-20 µm, but with some pores up to 100 µm across. SEM data confirmed the porometry results and demonstrated the different structures of the materials. Therefore, both materials were characterized by an interconnected porous structure and provided conditions for the adhesion and vital activity of human ASCs in vitro. In an experimental model of rabbit shin bone defect, it was shown that, during the 6-month observation period, neither of the materials caused negative reactions in the experimental animals. By the end of the observation period, restoration of the defects in animals in both groups was completed, and elements of both materials were preserved in the defect areas. Data from morphological examinations and CT data demonstrated that the rate of rabbit bone tissue regeneration with the hybrid polymer was comparable to that with the osteoplastic matrix. Therefore, the hybrid polymer has good potential for use in further research and improvement in biomedical applications.

Features of Changes in the Structure and Properties of a Porous Polymer Material with Antibacterial Activity during Biodegradation in an In Vitro Model.

Hybrid porous polymers based on poly-EGDMA and polylactide containing vancomycin, the concentration of which in the polymer varied by two orders of magnitude, were synthesized. The processes of polymer biodegradation and vancomycin release were studied in the following model media: phosphate-buffered saline (PBS), trypsin-Versene solution, and trypsin-PBS solution. The maximum antibiotic release was recorded during the first 3 h of extraction. The duration of antibiotic escape from the polymer samples in trypsin-containing media varied from 3 to 22 days, depending on the antibiotic content of the polymer. Keeping samples of the hybrid polymer in trypsin-containing model media resulted in acidification of the solutions-after 45 days, up to a pH of 1.84 in the trypsin-Versene solution and up to pH 1.65 in the trypsin-PBS solution. Here, the time dependences of the vancomycin release from the polymer into the medium and the decrease in pH of the medium correlated. These data are also consistent with the results of a study of the dynamics of sample weight loss during extraction in the examined model media. However, while the polymer porosity increased from ~53 to ~60% the pore size changed insignificantly, over only 10 µm. The polymer samples were characterized by their antibacterial activity against Staphylococcus aureus, and this activity persisted for up to 21 days during biodegradation of the material, regardless of the medium type used in model. Surface-dependent human cells (dermal fibroblasts) adhere well, spread out, and maintain high viability on samples of the functionalized hybrid polymer, thus demonstrating its biocompatibility in vitro.

Purely elastic turbulence in pressure-driven channel flows.

Solutions of long, flexible polymer molecules are complex fluids that simultaneously exhibit fluid-like and solid-like behavior. When subjected to an external flow, dilute polymer solutions exhibit elastic turbulence-a unique, chaotic flow state absent in Newtonian fluids, like water. Unlike its Newtonian counterpart, elastic turbulence is caused by polymer molecules stretching and aligning in the flow, and can occur at vanishing inertia. While experimental realizations of elastic turbulence are well-documented, there is currently no understanding of its mechanism. Here, we present large-scale direct numerical simulations of elastic turbulence in pressure-driven flows through straight channels. We demonstrate that the transition to elastic turbulence is sub-critical, giving rise to spot-like flow structures that, further away from the transition, eventually spread throughout the domain. We provide evidence that elastic turbulence is organized around unstable coherent states that are localized close to the channel midplane.

Ligand-Induced Intramolecular Redox Diversity in Titanium Complexes with Acenaphthene-1,2-diimine.

A series of the chlorido and alkoxychlorido titanium complexes of the general formula (dpp-Bian)Ti(OiPr)nCl3-n, where dpp-Bian = 1,2-bis[(2,6-iPr2C6H3)imino]acenaphthene n = 0 (2), 1 (3), 2 (4), as well as (dpp-Bian)Ti(OiPr)2 (5) and (dpp-Bian)Ti(OiPr)Cl3 (3-Cl), were isolated and characterized using single-crystal X-ray diffraction analysis and spectroscopic studies combined with density functional theory (DFT) calculations. In the solid state, compounds 2-4 reveal a square-pyramidal geometry at the metal center supported with monoanionic dpp-Bian, whereas 3-Cl with a neutral diimine ligand and 5 bearing a dianionic enebisamide dpp-Bian show, respectively, an octahedral and tetrahedral coordination surrounding the metal ion. Paramagnetic complexes 2-4 exhibit electron paramagnetic resonance spectra in both toluene solution and solid state, confirming the transfer of spin density from the metal ion to the dpp-Bian ligand as the number of alkoxy groups increases. The increase in polarity of the Ti-N bonds in the row 2 < 3 < 4 contributes to enhanced stability of the metal complexes with respect to O-donor molecules. Thus, in tetrahydrofuran (THF), compounds 2 and 3 undergo reversible solvolysis, whereas complex 4 is stable. The charge and spin density distributions as well as molecular orbital energies in 2-4 were analyzed on the basis of DFT calculations which also provided information on the electronic transition energies, absorption band assignments, and thermodynamic parameters of the reactions between the complexes and THF.

Genome Studies in Four Species of Calendula L. (Asteraceae) Using Satellite DNAs as Chromosome Markers.

The taxonomically challenging genus Calendula L. (Asteraceae) includes lots of medicinal species characterized by their high morphological and karyological variability. For the first time, a repeatome analysis of a valuable medicinal plant Calendula officinalis L. was carried out using high-throughput genome DNA sequencing and RepeatExplorer/TAREAN pipelines. The FISH-based visualization of the 45S rDNA, 5S rDNA, and satellite DNAs of C. officinalis was performed on the chromosomes of C. officinalis, C. stellata Cav., C. tripterocarpa Rupr., and C. arvensis L. Three satellite DNAs were demonstrated to be new molecular chromosome markers to study the karyotype structure. Karyograms of the studied species were constructed, their ploidy status was specified, and their relationships were clarified. Our results showed that the C. officinalis karyotype differed from the karyotypes of the other three species, indicating its separate position in the Calendula phylogeny. However, the presence of common repeats revealed in the genomes of all the studied species could be related to their common origin. Our findings demonstrated that C. stellata contributed its genome to allotetraploid C. tripterocarpa, and C. arvensis is an allohexaploid hybrid between C. stellata and C. tripterocarpa. At the same time, further karyotype studies of various Calendula species are required to clarify the pathways of chromosomal reorganization that occurred during speciation.

Gas-phase preparation of azulene (C10H8) and naphthalene (C10H8) via the reaction of the resonantly stabilized fulvenallenyl and propargyl radicals.

Synthetic routes to the 10π Hückel aromatic azulene (C10H8) molecule, the simplest polycyclic aromatic hydrocarbon carrying an adjacent five- and seven-membered ring, have been of fundamental importance due to the role of azulene - a structural isomer of naphthalene - as an essential molecular building block of saddle-shaped carbonaceous nanostructures such as curved nanographenes and nanoribbons. Here, we report on the very first gas phase preparation of azulene by probing the gas-phase reaction between two resonantly stabilized radicals, fulvenallenyl and propargyl , in a molecular beam through isomer-resolved vacuum ultraviolet photoionization mass spectrometry. Augmented by electronic structure calculations, the novel Fulvenallenyl Addition Cyclization Aromatization (FACA) reaction mechanism affords a versatile concept for introducing the azulene moiety into polycyclic aromatic systems thus facilitating an understanding of barrierless molecular mass growth processes of saddle-shaped aromatics and eventually carbonaceous nanoparticles (soot, interstellar grains) in our universe.

Unconventional gas-phase preparation of the prototype polycyclic aromatic hydrocarbon naphthalene (C10H8) via the reaction of benzyl (C7H7) and propargyl (C3H3) radicals coupled with hydrogen-atom assisted isomerization.

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous in the interstellar medium and in meteorites such as Murchison and Allende and signify the missing link between resonantly stabilized free radicals and carbonaceous nanoparticles (soot particles, interstellar grains). However, the predicted lifetime of interstellar PAHs of some 108 years imply that PAHs should not exist in extraterrestrial environments suggesting that key mechanisms of their formation are elusive. Exploiting a microchemical reactor and coupling these data with computational fluid dynamics (CFD) simulations and kinetic modeling, we reveal through an isomer selective product detection that the reaction of the resonantly stabilized benzyl and the propargyl radicals synthesizes the simplest representative of PAHs - the 10π Hückel aromatic naphthalene (C10H8) molecule - via the novel Propargyl Addition-BenzAnnulation (PABA) mechanism. The gas-phase preparation of naphthalene affords a versatile concept of the reaction of combustion and astronomically abundant propargyl radicals with aromatic radicals carrying the radical center at the methylene moiety as a previously passed over source of aromatics in high temperature environments thus bringing us closer to an understanding of the aromatic universe we live in.

Yield-stress transition in suspensions of deformable droplets.

Yield-stress materials, which require a sufficiently large forcing to flow, are currently ill-understood theoretically. To gain insight into their yielding transition, we study numerically the rheology of a suspension of deformable droplets in 2D. We show that the suspension displays yield-stress behavior, with droplets remaining motionless below a critical body-force. In this phase, droplets jam to form an amorphous structure, whereas they order in the flowing phase. Yielding is linked to a percolation transition in the contacts of droplet-droplet overlaps and requires strict conservation of the droplet area to exist. Close to the transition, we find strong oscillations in the droplet motion that resemble those found experimentally in confined colloidal glasses. We show that even when droplets are static, the underlying solvent moves by permeation so that the viscosity of the composite system is never truly infinite, and its value ceases to be a bulk material property of the system.

Radical-Radical Reactions in Molecular Weight Growth: The Phenyl + Propargyl Reaction.

The mechanism for hydrocarbon ring growth in sooting environments is still the subject of considerable debate. The reaction of phenyl radical (C6H5) with propargyl radical (H2CCCH) provides an important prototype for radical-radical ring-growth pathways. We studied this reaction experimentally over the temperature range of 300-1000 K and pressure range of 4-10 Torr using time-resolved multiplexed photoionization mass spectrometry. We detect both the C9H8 and C9H7 + H product channels and report experimental isomer-resolved product branching fractions for the C9H8 product. We compare these experiments to theoretical kinetics predictions from a recently published study augmented by new calculations. These ab initio transition state theory-based master equation calculations employ high-quality potential energy surfaces, conventional transition state theory for the tight transition states, and direct CASPT2-based variable reaction coordinate transition state theory (VRC-TST) for the barrierless channels. At 300 K only the direct adducts from radical-radical addition are observed, with good agreement between experimental and theoretical branching fractions, supporting the VRC-TST calculations of the barrierless entrance channel. As the temperature is increased to 1000 K we observe two additional isomers, including indene, a two-ring polycyclic aromatic hydrocarbon, and a small amount of bimolecular products C9H7 + H. Our calculated branching fractions for the phenyl + propargyl reaction predict significantly less indene than observed experimentally. We present further calculations and experimental evidence that the most likely cause of this discrepancy is the contribution of H atom reactions, both H + indenyl (C9H7) recombination to indene and H-assisted isomerization that converts less stable C9H8 isomers into indene. Especially at low pressures typical of laboratory investigations, H-atom-assisted isomerization needs to be considered. Regardless, the experimental observation of indene demonstrates that the title reaction leads, either directly or indirectly, to the formation of the second ring in polycyclic aromatic hydrocarbons.

Active turbulence and spontaneous phase separation in inhomogeneous extensile active gels.

We report numerical results for the hydrodynamics of inhomogeneous lyotropic and extensile active nematic gels. By simulating the coupled Cahn-Hilliard, Navier-Stokes, and Beris-Edwards equation for the evolution of the composition, flow and orientational order of an active nematic, we ask whether composition variations are important to determine its emergent physics. As in active gels of uniform composition, we find that increasing either activity or nematic tendency (e.g., overall active matter concentration) triggers a transition between an isotropic passive phase and an active nematic one. We show that composition inhomogeneities are important in the latter phase, where we find three types of possible dynamical regimes. First, we observe regular patterns with defects and vortices: these exist close to the passive-active transition. Second, for larger activity, or deeper in the nematic phase, we find active turbulence, as in active gels of uniform composition, but with exceedingly large composition variation. In the third regime, which is uniquely associated with inhomogeneity and occurs for large nematic tendency and low activity, we observe spontaneous microphase separation into active and passive domains. The microphase separated regime is notable in view of the absence of an explicit demixing term in the underlying free energy which we use, and we provide a theoretical analysis based on the common tangent construction which explains its existence. We hope this regime can be probed experimentally in the future.

Acceleration of a Chemical Reaction due to Nonequilibrium Collisional Dynamics: Dimerization of Polyaromatics.

Nonequilibrium precursor mediated kinetics has been discovered for reactions of gaseous molecules at high temperatures. A theoretical analysis was carried out on dimerization of midsize polycyclic aromatic hydrocarbons (PAH), the presumed critical step in formation of carbonaceous particles in terrestrial and extraterrestrial environments. The nonequilibrium precursor state originates from inelastic collisional dynamics of two PAH monomers, with low-frequency modes acting as a sink for translational energy in the reaction coordinate. Owing to the prolonged lifetime of the nonequilibrium physical dimer, the probability of chemical dimerization increases by an order of magnitude. This phenomenon brings us closer to a solution for the carbon-particle inception puzzle and should prove useful for the fundamental understanding of gas-phase chemical reactions involving large molecules.

Agro-Morphological and Cytogenetic Characterization of Colchicine-Induced Tetraploid Plants of Polemonium caeruleum L. (Polemoniaceae).

Polemonium caeruleum L. (Polemoniaceae) is a valuable medicinal herb with a wide spectrum of biological activities. Under natural conditions, the productivity of this species is rather low. In this study, colchicine-induced tetraploid plants (2n = 4x = 36) of P. caeruleum were obtained, and for the first time, their morphological and cytogenetic characterization was performed. In the tetraploid plants, raw material productivity and also the content of triterpene saponins were significantly higher than in the control diploids. The analysis of chromosome behavior at meiosis and FISH chromosome mapping of 45S and 5S rDNA generally demonstrated stability of both genomes in the tetraploid plants. Based on chromosome morphology and distribution patterns of the studied molecular cytogenetic markers, all chromosome pairs in karyotypes were identified, and chromosome karyograms and idiograms of P. caeruleum were constructed. The revealed specific microdiagnostic characteristics of P. caeruleum (strongly sinuous cells and anomocytic stomata of the leaf epidermis, and also glandular hairs along the veins) could be useful for raw material identification. In the obtained tetraploids, the predominance of large stomata on the lower leaf epidermis was determined. The studied tetraploids can be used in various breeding programs to obtain high-quality pharmaceutical raw materials of P. caeruleum.

Direct and Water-Mediated Adsorption of Stabilizers on SERS-Active Colloidal Bimetallic Plasmonic Nanomaterials: Insight into Citrate-AuAg Interactions from DFT Calculations.

In previous studies, AuAg colloidal nanostar formulations were developed with the two-fold aim of producing optimized surface-enhanced Raman spectroscopy (SERS) substrates and investigating the nature of the capping process itself. Findings demonstrated that the nanoparticle metals are alloyed and neutral, and capping by stabilizers occurs via chemisorption. This study utilizes citrate as the model stabilizer and investigates the mechanistic aspects of its interaction with mono- (Au20) and bimetallic (Au19Ag) surfaces by density functional theory (DFT) calculations. Citrate was modeled according to the colloid's pH and surrounded by a water and sodium first solvation shell. A population of stable cluster-citrate structures was obtained, and energies were refined at the uB3LYP//LANL2TZ(f)/cc-pVTZ level of theory. Solvation was accounted for both explicitly and implicitly by the application of the continuum model SMD. Results indicate that both direct binding and binding by water proxy through the charge-transfer complex formation are thermodynamically favorable. Water participation in citrate adsorption is supported by the adsorption behavior observed experimentally and the comparison between experimental and DFT-simulated IR spectra. Vibrational mode analysis suggests the possible presence of water within a crystal in dried nanostar residues. All ΔGads(aq) indicate a weak chemisorptive process, leading to the hypothesis that citrate could be displaced by analytes during SERS measurements.

Coherent Structures in Plane Channel Flow of Dilute Polymer Solutions with Vanishing Inertia.

When subjected to sufficiently strong velocity gradients, solutions of long, flexible polymers exhibit flow instabilities and chaotic motion, often referred to as elastic turbulence. Its mechanism differs from the familiar, inertia-driven turbulence in Newtonian fluids and is poorly understood. Here, we demonstrate that the dynamics of purely elastic pressure-driven channel flows of dilute polymer solutions are organized by exact coherent structures that take the form of two-dimensional traveling waves. Our results demonstrate that no linear instability is required to sustain such traveling wave solutions and that their origin is purely elastic in nature. We show that the associated stress profiles are characterized by thin, filamentlike arrangements of polymer stretch, which is sustained by a solitary pair of vortices. We discuss the implications of the traveling wave solutions for the transition to elastic turbulence in straight channels and propose ways for their detection in experiments.

Chromatographic framework for coffee ring effect-driven separation of small molecules in surface enhanced Raman spectroscopy analysis.

The applications of coffee ring effect (CRE) in analytical chemistry have been increasingly expanded from particles and macromolecules to small molecules, in particular coupled to surface-enhanced Raman spectroscopy (SERS). Despite the theory behind the formation of CRE itself from a single drop evaporation onto the dry surface is well established, the theoretical aspects of CRE-driven separation, especially the analyte-surface interactions involving small molecules, have not been conceived. Herein, we have developed a theoretical framework to describe the CRE-driven separation process of small molecules, using SERS analysis of dimethylarsinic acid (DMAV), dimethylmonothioarsinic acid (DMMTAV), and dimethyldithioarsinic acid (DMDTAV) on gold nanofilm (AuNF) as an example. By combining the CRE theory for the radial flow and the Extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory for mass transfer between solution and AuNF surface, we adapted the conventional chromatographic theory to derive a modified van Deemter equation for the CRE-driven separation. By using this model, we predicted the travel distances of arsenicals based on the different affinity of analytes to the AuNF and evaluated the possibility of separation of unknown analytes by CRE-based SERS, demonstrating the successful adaptation of classic chromatographic theory to CRE-driven nanochromatography.

The Reaction of o-Benzyne with Vinylacetylene: An Unexplored Way to Produce Naphthalene.

The mechanism and kinetics of the reaction of ortho-benzyne with vinylacetylene have been studied by ab initio and density functional CCSD(T)-F12/cc-pVTZ-f12//B3LYP/6-311G(d,p) calculations of the pertinent potential energy surface combined with Rice-Ramsperger-Kassel-Marcus - Master Equation calculations of reaction rate constants at various temperatures and pressures. Under prevailing combustion conditions, the reaction has been shown to predominantly proceed by the biradical acetylenic mechanism initiated by the addition of C4 H4 to one of the C atoms of the triple bond in ortho-benzyne by the acetylenic end, with a significant contribution of the concerted addition mechanism. Following the initial reaction steps, an extra six-membered ring is produced and the rearrangement of H atoms in this new ring leads to the formation of naphthalene, which can further dissociate to 1- or 2-naphthyl radicals. The o-C6 H4 +C4 H4 reaction is highly exothermic, by ∼143 kcal/mol to form naphthalene and by 31-32 kcal mol-1 to produce naphthyl radicals plus H, but features relatively high entrance barriers of 9-11 kcal mol-1 . Although the reaction is rather slow, much slower than the reaction of phenyl radical with vinylacetylene, it forms naphthalene and 1- and 2-naphthyl radicals directly, with their relative yields controlled by the temperature and pressure, and thus represents a viable source of the naphthalene core under conditions where ortho-benzyne and vinylacetylene are available.