Kinetic Rate Research Articles

Citrullination at the N-terminal region of MDM2 by the PADI4 enzyme.

PADI4 is one of the human isoforms of a family of enzymes involved in the conversion of arginine to citrulline. MDM2 is an E3 ubiquitin ligase that is critical for degradation of the tumor suppressor gene p53. We have previously shown that there is an interaction between MDM2 and PADI4 in cellulo, and that such interaction occurs through the N-terminal region of MDM2, N-MDM2, and in particular through residues Thr26, Val28, Phe91, and Lys98. Here, by using a "divide-and-conquer" approach, we have designed and synthesized peptides comprising these two polypeptide stretches (residues Ala21-Lys36, and Lys94-Val108), either in the wild-type species or in their citrullinated versions. Some of the citrullinated peptides were aggregation-prone, as suggested by DOSY-NMR experiments, but the wild-type versions of both fragments were monomeric in solution. We found out that wild-type and modified peptides were disordered in all cases, as also tested by far-UV circular dichroism (CD), and citrullination mainly affected the NMR chemical shifts of adjacent residues. Isothermal titration calorimetry (ITC) in the absence and presence of GSK484, an enzymatic PADI4 inhibitor, indicated that this compound blocked binding of the peptides to the enzyme. Binding to the active site of the N-MDM2 fragments was also confirmed by in silico experiments. The affinities of PADI4 for the wild-type peptides were more favorable than those of the corresponding citrullinated ones, but all measured values were within the micromolar range, indicating that there were no major variations in the thermodynamics of binding due to sequence effects. The kinetic dissociation rates, koff, measured by biolayer interferometry (BLI), were always one-order of magnitude faster for the citrullinated peptides than for the wild-type ones. Taken together, all these findings indicate that MDM2 is a substrate for PADI4 and is prone to citrullination in the identified (and specific) positions of its N-terminal region.

Rapid photocatalytic degradation of selective organic dyes using metal oxide-metal sulphide and its inverted nanocomposites

The chemical precipitation approach was employed to synthesize novel heterostructures, namely CeO2-ZnS and SnO2-ZnS, along with inverted nanocomposites ZnS-CeO2 and ZnS-SnO2. The nanocomposites were subjected to characterization using various techniques, including X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), UV–Vis absorption spectra, and photoluminescence spectra. The TEM images demonstrated particles that were homogeneous, well-dispersed, and comparatively tiny with a sphere-like structure. This indicates successful synthesis and desirable morphological properties of the nanocomposites. The integration of varied nanoparticles within a heterostructure commonly gives rise to synergistic effects, imparting superior properties to the composite compared to the individual components. These nanocomposites tested for their photocatalytic degradation efficiency using Rose Bengal (RB) and Crystal Violet (CV) dyes under natural sunlight and they exhibited approximately 95 % degradation rate. The degradation results demonstrated a significant enhancement in the photocatalytic efficiency of ZnS-CeO2 and CeO2-ZnS nanocomposites. This improvement was attributed to the effective recombination suppression of photogenerated electron-hole pairs, leading to the generation of highly reactive free radicals. The first-order kinetic rate constant for CeO2-ZnS was determined to be 0.52 min−1 for CV and 0.53 min−1 for RB. The present research work has the potential to offer a novel approach to the construction of new heterojunction photocatalysts and to provide a more profound understanding of the treatment of textile organic dyes.

Catalytic degradation of Rhodamine B through peroxymonosulfate activation by the Co-doped hydroxyapatite.

Supported Co-based catalysts have shown attractive prospects for peroxymonosulfate (PMS) activation. In this work, Co-doped hydroxyapatite (H-Co/HAP) composites were prepared by a simple hydrothermal method. The Co content in H-Co/HAP could reach 71.2mg/g, while the Co leaching rate remained relatively low. By right of the excellent catalytic performance, the as-prepared H-Co/HAP could achieve 99.02% degradation of Rhodamine B (RhB) within 10min in the presence of 0.5mM PMS and a first-order kinetic rate constant of 0.876min-1. Even after 8 cycles, the RhB degradation efficiency remained at 81.96%. In addition, the effects of vital reaction parameters, including catalyst dosage, PMS dosage, initial pH, humic acid, and coexisting anions, on the catalytic performance in the H-Co/HAP10/PMS system were systematically investigated and discussed. The degradation mechanism of a non-radical (1O2) as the dominant active specie and a radical (•O2- and SO4•-) as the minor active specie was identified through quenching experiments and electron paramagnetic resonance testing. Moreover, possible degradation pathways of RhB were proposed in the H-Co/HAP10/PMS system. Overall, this study offers a meaningful strategy for designing high-content Co-based catalysts to degrade dye molecules in wastewater.

Development, analysis, and effectiveness of an F-C-MgO/rGOP catalyst for the degradation of atrazine using ozonation process: Synergistic effect, mechanism, and toxicity assessment.

This study considered the effects of fluoride, MgO, sucrose, and rGO on the characteristics of the fluoride-carbon-MgO/rGO predicted (F-C-MgO/rGOP) catalyst and its effectiveness in the catalytic ozonation process (COP) for atrazine elimination from aqueous solutions. Using a mixture design, the catalyst composition was optimized to 13.6% sucrose, 50% Mg (OH)2, 25% NaF, and 11.4% rGO, which demonstrated the highest catalytic activity for atrazine degradation. Analysis of the synthesized F-C-MgO/rGO revealed a mesoporous structure with a BET surface area of 145m2/g. The optimized COP parameters were a pH of 8.5, contact time of 11min, catalyst dose of 1.38g/L, and atrazine concentration of 10mg/L. Atrazine mineralization reached 62.8% after 15min of contact time. The COP exhibited a synergistic effect of 82.5%, a mineralization capacity of 17.75mg/g, and a kinetic rate constant of 0.25min⁻1 for atrazine degradation. Intermediate analysis identified alkyl oxidation, dealkylation, and dechlorination-hydroxylation as the main pathways of degradation. Biodegradability index and toxicity assessments indicated a reduction in the toxicity of treated wastewater (both synthetic and real) after COP treatment. A BOD₅/COD ratio above 0.5 in both samples indicated the wastewater was suitably biodegradable.

Regulating the Thermodynamic Uniformity and Kinetic Diffusion of Zinc Anodes for Deep Cycling of Ah-Level Aqueous Zinc-Metal Batteries.

Zn metal anodes in mildly acidic electrolytes usually suffer from a series of problems, including parasitic dendrite growth and severe side reactions, significantly limiting the Zn utilization efficiency and cycling life. A deep understanding of the Zn stripping/plating process is essential to obtain high-efficiency and long-life Zn metal anodes. Here, the factors affecting the Zn stripping/plating process are revealed, suggesting that thermodynamic uniformity in bulk structures promotes an orderly Zn stripping process, and a fast kinetic diffusion rate on the Zn surface facilitates uniform Zn deposition. Then, a bulk and surface co-optimized strategy for stabilizing Zn metal anodes is proposed, which is confirmed to effectively suppress the Zn dendrite growth and side reactions. Thus, the modified Zn anodes display record-breaking cycling lives of 1200 and 200 h under ultrahigh Zn utilization efficiencies of 80 and 93.5%, respectively. More importantly, using this modified Zn metal anode enables us to realize Ah-level pouch cells for continuous cycles under harsh conditions.

{110} Surface-Exposed Bi3.15Nd0.85Ti3O12 Ferroelectric Nanosheet Arrays on Porous Ceramics as Efficient and Recyclable Piezo-Photocatalysts.

Bismuth-layered ferroelectric nanomaterials exhibit great potential for piezo-photocatalysis. However, a major challenge lies in the difficulty of recovering the catalytic powders, raising concerns regarding secondary pollution of water. In this work, a novel hierarchical porous ferroelectric ceramic containing {110} surface-exposed Bi3.15Nd0.85Ti3O12 (BIT-Nd) nanosheet arrays is grown on a porous ceramic matrix for efficient and recyclable piezo-photocatalysis. By controlling the BIT-Nd loading level of the nanosheets, the piezo-photocatalytic degradation efficiency of a Rhodamine B(RhB)(C0 = 10 mgL-1) solution reached an optimum value of 97.1% in 100 min with a first-order kinetic rate constant, k, of up to 0.0321 min-1 in Bi3.15Nd0.85Ti3O12-20 (BITNd-20) with a mass ratio of hydrothermal products to ceramics of 20%. In the presence of BITNd-20, a surprising H2 yield rate of 130 µmol·h-1 is achieved without using anycocatalyst or scavenger. Specially, the beneficial role of snowflake structures on piezoelectric potential amplification and introducing nanosheets with exposed {110} surfaces on hydrogen evolution reaction (HER) activity, piezoelectric potential output, and catalytic performance of porous ceramics has been revealed. This unique design strategy provides a new approach to enhance the piezo-photocatalytic activity by addressing environmental issues and enhancing catalytic performance to yield cleaner energy.

Experiment-Guided Refinement of Milestoning Network.

Milestoning is an efficient method for calculating rare event kinetics by constructing a continuous-time kinetic network that connects the reactant and product states. Its accuracy depends on both the quality of the underlying force fields and the trajectory sampling. The sampling error can be effectively controlled through various methods. However, the force fields are often not accurate enough, leading to quantitative discrepancies between simulations and experimental data. To address this challenge, we present a refinement approach for Milestoning network based on the maximum caliber (MaxCal), a general variational principle for dynamical systems, to combine simulations and experimental data. The Kullback-Leibler divergence rate between two Milestoning networks is analytically evaluated and minimized as the loss function. Meanwhile, experimental thermodynamic (equilibrium constants) and kinetic (rate constants) data are incorporated as constraints. The use of MaxCal implies that the refined kinetic network is minimally perturbed from the original one while satisfying the experimental constraints. The refined network is expected to align better with available experimental data. The refinement approach is demonstrated using the binding and unbinding dynamics of a series of six small molecule ligands for the model host system, β-cyclodextrin.

Non-metallic iodine single-atom catalysts with optimized electronic structures for efficient Fenton-like reactions

In this study, we introduce a highly effective non-metallic iodine single-atom catalyst (SAC), referred to as I-NC, which is strategically confined within a nitrogen-doped carbon (NC) scaffold. This configuration features a distinctive C-I coordination that optimizes the electronic structure of the nitrogen-adjacent carbon sites. As a result, this arrangement enhances electron transfer from peroxymonosulfate (PMS) to the active sites, particularly the electron-deficient carbon. This electron transfer is followed by a deprotonation process that generates the peroxymonosulfate radical (SO5•−). Subsequently, the SO5•− radical undergoes a disproportionation reaction, leading to the production of singlet oxygen (1O2). Furthermore, the energy barrier for the rate-limiting step of SO5•− generation in I-NC is significantly lower at 1.45 eV, compared to 1.65 eV in the NC scaffold. This reduction in energy barrier effectively overcomes kinetic obstacles, thereby facilitating an enhanced generation of 1O2. Consequently, the I-NC catalyst exhibits remarkable catalytic efficiency and unmatched reactivity for PMS activation. This leads to a significantly accelerated degradation of pollutants, evidenced by a relatively high observed kinetic rate constant (kobs ~ 0.436 min−1) compared to other metallic SACs. This study offers valuable insights into the rational design of effective non-metallic SACs, showcasing their promising potential for Fenton-like reactions in water treatment applications.

Programmable DNA Nanoswitch-Regulated Plasmonic CRISPR/Cas12a-Gold Nanostars Reporter Platform for Nucleic Acid and Non-Nucleic Acid Biomarker Analysis Assisted by a Spatial Confinement Effect.

CRISPR/Cas 12a system based nucleic acid and non-nucleic acid targets detection faces two challenges including (1) multiple crRNAs are needed for multiple biomarkers detection and (2) insufficient sensitivity resulted from photobleaching of fluorescent dyes and the low kinetic cleavage rate for a traditional single-strand (ssDNA) reporter. To address these limitations, we developed a programmable DNA nanoswitch (NS)-regulated plasmonic CRISPR/Cas12a-gold nanostars (Au NSTs) reporter platform for detection of nucleic acid and non-nucleic acid biomarkers with the assistance of the spatial confinement effect. Through simply programming the target recognition sequence in NS, only one crRNA is required to detect both nucleic acid and non-nucleic acid biomarkers. The detection limit decreased by ∼196-fold for miRNA-375 and 122-fold for prostate-specific antigen (PSA), respectively. Moreover, versatile evaluation of miRNA-375 and PSA in clinical urine samples can also be achieved, according to which prostate cancer and healthy groups can be well identified.

WeTICA: A directed search weighted ensemble based enhanced sampling method to estimate rare event kinetics in a reduced dimensional space.

Estimating rare event kinetics from molecular dynamics simulations is a non-trivial task despite the great advances in enhanced sampling methods. Weighted Ensemble (WE) simulation, a special class of enhanced sampling techniques, offers a way to directly calculate kinetic rate constants from biased trajectories without the need to modify the underlying energy landscape using bias potentials. Conventional WE algorithms use different binning schemes to partition the collective variable (CV) space separating the two metastable states of interest. In this work, we have developed a new "binless" WE simulation algorithm to bypass the hurdles of optimizing binning procedures. Our proposed protocol (WeTICA) uses a low-dimensional CV space to drive the WE simulation toward the specified target state. We have applied this new algorithm to recover the unfolding kinetics of three proteins: (A) TC5b Trp-cage mutant, (B) TC10b Trp-cage mutant, and (C) Protein G, with unfolding times spanning the range between 3and40μs using projections along predefined fixed Time-lagged Independent Component Analysis (TICA) eigenvectors as CVs. Calculated unfolding times converge to the reported values with good accuracy with more than one order of magnitude less cumulative WE simulation time than the unfolding time scales with or without a priori knowledge of the CVs that can capture unfolding. Our algorithm can be used with other linear CVs, not limited to TICA. Moreover, the new walker selection criteria for resampling employed in this algorithm can be used on more sophisticated nonlinear CV space for further improvements of binless WE methods.

Carbon nanotube/bentonite @ polyvinylidene fluoride tri-flouro ethylene nanocomposite matrix for surpior elimination of carcinogenic dye from wastewater

Abstract This study examines the sorption behavior of Congo Red (CR) dye from water-based solutions using a synergistic nanocomposite made of Bentonite (BT), multi-walled carbon nanotubes (MWCNTs), and a Poly (vinylidene fluoride tri-flouroethylene) (P(VDF-TRFE)) polymer matrix with exceptional adsorption capacity for the selective removal of Congo red dye from aqueous solutions. This is done in order to address the urgent concerns surrounding the health and environmental implications of CR dye. Utilizing modern analytical technique such as FTIR, XRD, SEM, TEM, and TGA, the adsorption physicochemical interaction and nanocomposite manufacturing were carefully investigated, offering thorough insights into the composite's general properties. Nanocomposite structures of between 31 and 37 nm in diameter were discovered by TEM examination. The adsorption process was pH dependent, reaching a peak removal effectiveness of 94.5% at pH 3.0. The correlation coefficients obtained from kinetic modeling using pseudo-first-order and pseudo-second-order equations were 0.97389 and 0.96802, respectively, suggesting that the adsorption mechanism adhered to first-order rate kinetics. Thermodynamic investigation revealed an exothermic and spontaneous reaction, with a negative ΔG value between − 7.45 and − 7.95 J/mol. The nanocomposite outperformed the capacities reported for individual components in earlier investigations, with an impressive monolayer sorption capacity (qmax) of 143.88 mg/g. As a result, there is great potential for this innovative nanocomposite to be a very successful adsorbent for treating industrial wastewater. Graphical Abstract

Mechanism, Performance, and Application of g-C3N5-Coupled TiO2 as an S-Scheme Heterojunction Photocatalyst for the Abatement of Gaseous Benzene.

In this research, S-scheme heterojunction photocatalysts are prepared through the hybridization of nitrogen-rich g-C3N5 with TiO2 (coded as TCN5-(x): x as the weight ratio of TiO2:g-C3N5). The photocatalytic potential of TCN5-(x) is evaluated against benzene (1-5 ppm) across varying humidity levels using a dynamic flow packed-bed photocatalytic reactor. Among the prepared composites, TCN5-(10) exhibits the highest synergy between g-C3N5 and TiO2 at "x" ratio of 10%, showing superior best benzene degradation performance (e.g., 93.9% removal efficiency, specific clean air delivery rate of 1126.9 L g-1 h-1, kinetic reaction rate of 46.1 nmol mg-1 min-1, quantum yield of 6.0 × 10-4 molec. photon-1, and space-time yield of 1.2 × 10-4 molec. photon-1 mg-1). The formation of an S-scheme heterojunction with a built-in internal electric field is supported by both theoretical (through the density functional theory calculations) and photoelectrochemical bases (e.g., improvement in the band potential and electrochemistry along with surface characteristics (e.g., reactive sites and charge migrations at the interface)). The results of the in situ DRIFTS analysis confirm that the oxidation of benzene molecules is accompanied by many reaction intermediates (e.g., phenolate, maleate, acetate, and methylene). The outcomes of this work will help us pursue the development of a state-of-the-art photocatalytic system for air quality management.

Correlation between sarcopenia and hypertrophy of the future liver remnant in patients undergoing portal vein embolization before liver resection.

To study the correlation between sarcopenia and hypertrophy of the future liver remnant(FLR) in patients undergoing portal vein embolization(PVE) before liver resection, and to assess the outcomes after resection. This retrospective study examined patients underwent PVE from May 2012 to May 2023. Demographic, clinical and laboratory features were documented and total liver volumes(TLV) and FLR volumes were measured before and 2-4 weeks after PVE. Degree of hypertrophy(DH), percentage hypertrophy(PH) and kinetic growth rate(KGR) of the FLR were calculated. Sarcopenia was defined using the skeletal muscle index(SMI) at the L3 vertebral level. Subcutaneous adipose index(SAI), visceral adipose index(VAI), cross sectional area of psoas muscle at the largest diameter(CSPM) and L3 vertebral level mean muscle attenuation(MA) were also assessed. Forty patients were included in the analysis and the median age was 57.5(IQR 51-64) and majority were males 27/40(67.5%). Twenty two patients were non-sarcopenics and 18 were sarcopenics. All patients showed hypertrophy of FLR(p = 0.001). SMI demonstrated moderate positive correlations with DH(r = 0.46, p = 0.003), PH(r = 0.47, p = 0.002) and KGR(r = 0.44, p = 0.004). VAI showed weak positive correlations with DH(r = 0.22, p = 0.17), PH(r = 0.18, p = 0.27), and KGR(r = 0.14, p = 0.37). Pre-PVE FLR demonstrated a weak negative correlation with PH(r=-0.35, p = 0.03) and KGR(r=-0.12, p = 0.47). Sarcopenia, specifically SMI, significantly correlates with FLR hypertrophy after PVE. Assessment of sarcopenia and body compartments prior to PVE could help in stratifying and treats patients with impaired FLR growth. This study with data spanning over 11-years, is the first in the Indian population to demonstrate a significant correlation between SMI, a marker of sarcopenia, and FLR hypertrophy following PVE.

Insight into the roles of Cl− for the degradation of acid Red 14 in an electrochemical advanced oxidation system: Mechanisms and DFT studies

Textile wastewater was typically characterized by high concentrations of chloride ions, with Acid Red 14 (AR14) representing a significant pollutant. Nevertheless, research into the degradation of AR14 by electrochemical advanced oxidation processes (EAOPs) had largely overlooked the influence of chloride ions. In this regard, the EC-Clorine-MMO/Ti system was designed, and the degradation mechanism of AR14 was subjected to meticulous investigation. The adopted anode was composed of Ti/IrO2-Ta2O5 (mixed metal oxide, MMO). It demonstrated superior efficiency in degrading AR14 within a sodium chloride (NaCl) electrolyte, registering an apparent kinetic constant rate approximately 16.76 times greater than that observed within a sodium perchlorate (NaClO4) electrolyte. The optimal chloride ion concentration was identified as 0.04 mol/L. Besides, alkaline conditions were not conducive to the degradation of AR14. It was noteworthy that the electrochemical byproducts chlorite (ClO2−), chlorate (ClO3−), perchlorate (ClO4−), and trihalomethane (THMs) were not produced in the solution treated by the EC-Clorine-MMO/Ti system. Electron paramagnetic resonance (EPR) spectroscopy, probe, and quenching experiments identified that hydroxyl radicals (•OH), superoxide radicals (O2•−), and dichloride radicals/chlorine monoxide radicals (Cl2•−/ ClO•) were the major reactive species. Of these, •OH played a pivotal role in AR14 degradation. Additionally, the three principal degradation pathways of AR14 were deduced by LC-MS analysis, UV–vis spectra, density-functional theory (DFT) calculations, and excitation-emission matrix (EEM) fluorescence spectroscopy. Furthermore, the generation mechanism of reactive species and the proposed mechanism of AR14 degradation by the EC-Clorine-MMO/Ti system were presented. The study made a significant contribution to the understanding of the electrochemical reactions occurring in textile wastewater and provided valuable insights into the rational control of electrolytic conditions for the treatment of saline wastewater.

Multi-perspective kinetic analysis of plastic blends under thermogravimetric pyrolysis conditions.

Plastic blends were co-pyrolyzed under non-isothermal conditions in a thermogravimetric (TG) analyzer. The co-pyrolysis characteristics and kinetic triplet, i.e., apparent activation energies, reaction models, and preexponential factors, were investigated from different perspectives, including the overall, weight-loss stage, and overlapping complex reaction deconvolution perspective. Fraser Suzuki (FS) deconvolution was adopted for the peak fitting of the differential TG curves. A model-free method and the master plot theory were used to solve the kinetic equations and fit the reaction mechanism models, respectively. The results indicated that the co-pyrolysis of plastic blends (polyvinyl chloride (PVC)/polypropylene, PVC/polystyrene, PVC/acrylonitrile-butadiene-styrene) could not be adequately described using the overall approach or the weight-loss stage approach. The pyrolysis reaction exhibited a complex multistep overlapping reaction mechanism. FS deconvolution identified and separated four pseudo-reactions from the pyrolysis reaction. The kinetic triplet of the separated reactions was estimated and used to establish kinetic rate equations. Mathematical relations were established between the mass loss rate and pyrolysis temperature. The TG curves of the co-pyrolysis of plastic blends can be parameterized and predicted using the overlapping complex reaction deconvolution model. This study can act as a basis for the development of thermal conversion of mixed plastic waste.

MXene decorated ZnO-tetrapod for efficient degradation of Methyl Orange, Methylene Blue, and Rhodamine B dyes

For the first time, Methyl Orange (MO), Methylene Blue (MB), and Rhodamine B (RhB) dyes degradation using MXene decorated ZnO-tetrapod (MZT) has been reported. MXene was derived from MAX phase using HF etching and ZT was produced using flame transport synthesis (FTS) technique. MXene was decorated on ZT using blending and sonication of deionized water consisting of MXene and ZT. The MZT was characterized using X-ray diffraction (XRD), UV–visible spectroscopy, Tauc plot analysis, Brunauer-Emmett-Teller (BET) surface area measurement, field emission scanning electron microscopy (FESEM) and High-Resolution Transmission Electron Microscopy (HRTEM) to ensure the successful decoration. The dye degradation capability of the MZT was tested against three dyes: MO, MB, and RhB. Photodegradation tests under sunlight showed RhB had the highest efficiency (77.60 %), followed by MO (76.79 %) and MB (50.83 %), respectively. The kinetic rate constants confirmed RhB’s superior degradation. Furthermore, Electron paramagnetic resonance (EPR) spectroscopy revealed oxygen vacancies, enhancing photocatalytic performance. MZT maintained high efficiency, with less than 20 % loss after 4 cycles, demonstrating its potential for repeated use in wastewater treatment and environmental pollution mitigation. The results reveal the potential of MZT in photocatalytic degradation of harmful organic dyes, very promising solution for combating environmental pollution.

Strongly coupled and highly-compacted zirconium aminobenzenedicarboxylate crystal membranes for accelerating carbon dioxide capture.

This study presents the fabrication of a UiO-66-NH2 composite membrane on a porous carbon cloth-polypyrrole substrate (CC-PPy@UiO-66-NH2) that demonstrates strongly coupled and highly ordered features to enhance CO2 capture efficiency. This free-standing configuration exhibits a higher adsorption kinetics with a slope of 0.48 mg g-1 min-1 for CO2 and superior adsorption selectivity, demonstrating that the adsorption kinetics rate of the CC-PPy@UiO-66-NH2 composite membrane for CO2 is approximately twice that of bulk UiO-66-NH2 (0.27 mg g-1 min-1) crystals at a bar.

Mathematical Modeling for Oscillations Driven by Noncoding RNAs.

In this chapter, we first survey strategies for the mathematical modeling of gene regulatory networks for capturing physiologically important dynamics in cells such as oscillations. We focus on models based on ordinary differential equations with various forms of nonlinear functions that describe gene regulations. We next use a small system of a microRNA and its mRNA target to illustrate a recently discovered oscillator driven by noncoding RNAs. This oscillator has unique features that distinguish it from conventional biological oscillators, including the absence of an imposed negative feedback loop and the divergence of the periods. The latter property may serve crucial biological functions for restoring heterogeneity of cell populations on the timescale of days. We describe general requirements for obtaining the limit cycle oscillations in terms of underlying biochemical reactions and kinetic rate constants. We discuss future directions stemming from this minimal, noncoding RNA-based model for gene expression oscillation.

Electrochemical nucleation and growth kinetics: insights from single particle scanning electrochemical cell microscopy studies.

The kinetics of particle nucleation and growth are critical to a wide variety of electrochemical systems. While studies carried out at the single particle level are promising for improving our understanding of nucleation and growth processes, conventional analytical frameworks commonly employed in bulk studies may not be appropriate for single particle experiments. Here, we present scanning electrochemical cell microscopy (SECCM) studies of Ag nucleation and growth on carbon and indium tin oxide (ITO) electrodes. Statistical analyses of the data from these experiments reveal significant discrepancies with traditional, quasi-equilibrium kinetic models commonly employed in the analysis of particle nucleation in electrochemical systems. Time-dependent kinetic models are presented capable of appropriately analysing the data generated via SECCM to extract meaningful chemical quantities such as surface energies and kinetic rate constants. These results demonstrate a powerful new approach to the analysis of single particle nucleation and growth data which could be leveraged in differentiating behavior within spatially heterogeneous systems.

High-throughput approach to measure number of nanoparticles associated with cells: size dependence and kinetic parameters.

Understanding how nanoparticle properties influence uptake by cells is highly important for developing nanomedicine design principles. For this, quantitative studies where actual numbers of cell-associated particles are determined are highly relevant. However, many techniques able to measure particle numbers suffer from low-throughput or place requirements on the types of nanoparticles that can be measured. Here we show the usage of flow cytometry to measure numbers of cell-associated nanoparticles for particles ranging in size from 100-500 nm, and extend this range to 40-500 nm by separate calibration. For the 100 nm particles, we corroborate the numbers by direct, low-throughput, counting using fluorescence microscopy. Applying flow cytometry we subsequently investigated the effect of particle size on the number of cell-associated particles for various timespans up to 5 h and found only a minor effect of size between 40, 100, and 200 nm particles. Next, we measured the kinetic rate constants describing the adsorption, desorption, and internalization for the 100 nm particles specifically. In general, we found values in accordance with previous literature. We foresee the future usage of the methodology applied here to investigate the kinetics of nanoparticle cellular uptake for a variety of particle types.