Function Of Experimental Conditions Research Articles

Probabilistic deconvolution of the distribution of relaxation times from multiple electrochemical impedance spectra

Electrochemical impedance spectroscopy (EIS) is widely used to study the properties of electrochemical materials and systems. However, analyzing EIS data remains challenging. Among various analysis methods, the distribution of relaxation times (DRT) has emerged as a novel non-parametric approach capable of providing timescale information. Among the various DRT inversion methods, those based on Gaussian processes (GP) are particularly promising because they provide uncertainty estimates for both EIS and DRT. However, current GP-based DRT implementations can only handle one spectrum at a time. This work extends these models to allow concurrent analysis of multiple impedance spectra as a function of experimental conditions. The new method, called the quasi-Gaussian process distribution of relaxation times, treats the DRT as a GP with respect to the experimental state and as a finite approximation of a positively constrained GP with respect to timescales. This new DRT inversion approach is validated against noise-corrupted artificial EIS data and applied to experimental data, allowing us to expedite EIS data analysis of multiple EIS data from a probabilistic perspective.

A nanoscale study of hafnium oxide resistive memory switching dynamics

This paper deals with the set and reset time measurements of a resistive memory consisting of a Ti/TiN/HfO2 layer stack contacted with the tip of a conductive atomic force microscope in ultra high vacuum. We present measurements of the set and reset switching times in voltage pulse regime for different voltages and compliance currents. The experimental results are well reproduced by simulation. We derive analytical expressions for the set and reset times as function of experimental conditions. The effect of voltage and current on reset and set switching times is then discussed with the help of their analytical expressions, which are also applied on standard devices characteristics.

Tunable High Entropy Lanthanide Oxide Microspheres via Confined Electroprecipitation in Emulsion Droplet Scaffolds.

Emergent high entropy nanomaterials and their associated complex surface structure hold promise to unlock unique catalytic intermediate pathways and photonic/plasmonic interactions; however, synthetic strategies to tune the size, morphological, and stoichiometric properties remain limited. This work demonstrates a confined electro-precipitation mechanism for the formation of tunable, high-entropy oxide microspheres within emulsion droplet scaffolds. This mechanism complements a traditional confined electrodeposition mechanism and explains the previously observed anomalous formation of thermodynamically unfavorable particles, including lanthanide species. Mass transfer studies reveal that microsphere coverage over a surface may be tuned and modeled by using a time-dependent modified Levich equation. Additionally, morphological tuning was demonstrated as a function of experimental conditions, such as rotation rate and precursor concentration. Finally, extension to multimetallic species permitted the generation of high-entropy lanthanide oxide microspheres, which were confirmed to have equimolar stoichiometries via energy dispersive spectroscopy and inductively coupled plasma mass spectrometry. This novel method promises to generate tunable, complex oxides with applications to thermal catalysis, optics, and applications yet unknown.

Variability across subjects in free recall versus cued recall.

Memory scientists usually compare mean performance on some measure(s) (accuracy, confidence, latency) as a function of experimental condition. Some researchers have made within-subject variability in task performance a focal outcome measure (e.g., Yao et al., Journal of Clinical and Experimental Neuropsychology, 38, 227-237, 2016). Here, we explored between-subject variability in accuracy as a function of experimental conditions. This work was inspired by an incidental finding in a previous study, in which we observed greater variability in accuracy of memory performance on cued recall (CR) versus free recall (FR) of English animal/object nouns (Mah et al., Frontiers in Psychology, 14, 1146200, 2023). Here we report experiments designed to assess the reliability of that pattern and to explore its causes (e.g., differential interpretation of instructions, [un]relatedness of CR word pairs, encoding time). In Experiment 1 (N = 120 undergraduates), we replicated the CR:FR variability difference with a more representative set of English nouns. In Experiments 2A (N = 117 Prolific participants) and 2B (N = 127 undergraduates), we found that the CR:FR variability difference persisted in a forced-recall procedure. In Experiment 3 (N = 260 Prolific participants), we used meaningfully related word pairs and still found greater variability in CR than in FR performance. In Experiment 4 (N = 360 Prolific participants), we equated CR and FR study phases by having all participants study pairs and, again, observed greater variability in CR than FR. The same was true in Experiment 5 (N = 120 undergraduates), in which study time was self-paced. Comparisons of variability across subjects can yield insights into the mechanisms underlying task performance.

Internet-Delivered Dialectical Behavioral Therapy Skills Training for Chronic Pain: Protocol for a Randomized Controlled Trial.

Emotion dysregulation is key to the development and maintenance of chronic pain, feeding into a cycle of worsening pain and disability. Dialectical behavioral therapy (DBT), an evidence-based treatment for complex transdiagnostic conditions presenting with high emotion dysregulation, may be beneficial to manage and mitigate the emotional and sensory aspects of chronic pain. Increasingly, DBT skills training as a key component of standard DBT is being delivered as a stand-alone intervention without concurrent therapy to help develop skills for effective emotion regulation. A previous repeated-measure single-case trial investigating a novel technologically driven DBT skills training, internet-delivered DBT skills training for chronic pain (iDBT-Pain), revealed promising findings to improve both emotion dysregulation and pain intensity. This randomized controlled trial aims to examine the efficacy of iDBT-Pain in comparison with treatment as usual to reduce emotion dysregulation (primary outcome) for individuals with chronic pain after 9 weeks and at the 21-week follow-up. The secondary outcomes include pain intensity, pain interference, anxiety symptoms, depressive symptoms, perceived stress, posttraumatic stress, harm avoidance, social cognition, sleep quality, life satisfaction, and well-being. The trial also examines the acceptability of the iDBT-Pain intervention for future development and testing. A total of 48 people with chronic pain will be randomly assigned to 1 of 2 conditions: treatment and treatment as usual. Participants in the treatment condition will receive iDBT-Pain, consisting of 6 live web-based group sessions led by a DBT skills trainer and supervised by a registered psychologist and the iDBT-Pain app. Participants in the treatment-as-usual condition will not receive iDBT-Pain but will still access their usual medication and health interventions. We predict that iDBT-Pain will improve the primary outcome of emotion dysregulation and the secondary outcomes of pain intensity, pain interference, anxiety symptoms, depressive symptoms, perceived stress, harm avoidance, social cognition, sleep quality, life satisfaction, and well-being. A linear mixed model with random effects of individuals will be conducted to investigate the differences between the baseline, 9-week (primary end point), and 21-week (follow-up) assessments as a function of experimental condition. Recruitment started in February 2023, and the clinical trial started in March 2023. Data collection for the final assessment is planned to be completed by July 2024. If our hypothesis is confirmed, our findings will contribute to the evidence for the efficacy and acceptability of a viable intervention that may be used by health care professionals for people with chronic pain. The results will add to the chronic pain literature to inform about the potential benefits of DBT skills training for chronic pain and will contribute evidence about technologically driven interventions. Australian New Zealand Clinical Trials Registry ACTRN12622000113752; https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=383208&isReview=true. PRR1-10.2196/41890.

Recyclability of Vitrimer Materials: Impact of Catalyst and Processing Conditions.

With sustainability at the forefront of material research, recyclable polymers, such as vitrimers, have garnered increasing attention since their introduction in 2011. In addition to a traditional glass-transition temperature (Tg), vitrimers have a second topology freezing temperature (Tv) above which dynamic covalent bonds allow for rapid stress relaxation, self-healing, and shape reprogramming. Herein, we demonstrate the self-healing, shape memory, and shape reconfigurability properties as a function of experimental conditions, aiming toward recyclability and increased useful lifetime of the material. Of interest, we report the influence of processing conditions, which makes the material vulnerable to degradation. We report a decreased crosslink density with increased thermal cycling and compressive stress. Furthermore, we demonstrate that shape reconfigurability and self-healing are enhanced with increasing compressive stress and catalyst concentration, while their performance as a shape memory material remains unchanged. Though increasing the catalyst concentration, temperature, and compressive stress clearly enhances the recovery performance of vitrimers, we must emphasize its trade-off when considering the material degradation reported here. While vitrimers hold great promise as structural materials, it is vital to understand how experimental parameters impact their properties, stability, and reprocessability before vitrimers reach their true potential.

Chasing the desire: An investigation on the role of craving, time perspective, and alcohol use in adolescent gambling

Chasing, or continuing to gamble to recoup losses, is a behavioral marker and a diagnostic criterion for gambling disorder. Research on chasing has focused mainly on adults, whereas the analysis of chasing behavior among adolescents has not received empirical attention in the gambling literature. The aim of the present study was to first investigate the interplay between chasing behavior, craving, temporal perspective, alcohol use, and gambling severity among Italian adolescents. Three hundred and sixty-four adolescents took part in the study. Participants completed the South Oaks Gambling Screen Revised for Adolescents (SOGS-RA), the Gambling Craving Scale (GACS), the 14-item Consideration of Future Consequences scale (CFC-14), the Alcohol Use Disorders Identification Test (AUDIT), and performed a computerized task assessing chasing behavior. Participants were randomly assigned to the control and the loss condition of the computerized task. Results indicated that the choice to continue playing, as well as chasing frequency did not vary as a function of experimental condition. Hierarchical logistic and linear regression analyses revealed that the decision to chase depended mostly on craving, whereas chasing propensity was affected by craving and alcohol misuse. Notably, gambling severity did not predict either the decision to chase, or the chasing persistence. The present study contributes important findings to the gambling literature, highlighting the role of craving alcohol use in facilitating the inability to stop within-sessions gambling among adolescents. These findings may provide evidence that nonchasers and chasers represent two different types of gamblers, and that the difference may be useful for targeting more effective therapies.

A Short‐Chain Branching Distribution Determination Technique for Polyethylene Using IR5‐Detected GPC

AbstractIn this paper, a robust short‐chain branching (SCB) determination technique recently developed using IR5‐detected GPC (GPC‐IR5) for polyethylene resins is reported, wherein the IR5 detector is an infrared detector equipped with five filters set at different frequency ranges and a mercury‐cadmium‐telluride detector with thermoelectric cooling capability. Both intensity ratios of methyl/methylene and methyl/all C─H groups have very good linear relationship with the SCB content. Based on these relationships, an excel spreadsheet method is developed to deduce the SCB distribution across the molecular weight distribution using in‐house developed algorithms. The uncertainty of SCB determination using the GPC‐IR5 technique is found to be chromatographic signal‐to‐noise ratio dependent and can be explicitly expressed and calculated slice by slice. The SCB uncertainty is also found to be a function of experimental conditions and environment, which can affect not only the signals but also the noise levels at different IR bands. At a given polymer concentration, the higher the SCB content, the smaller the relative error bars. The SCB detection limit of this GPC‐IR5 technique is found to be at ≈0.5–1.0 SCB per 1000 TC for all samples tested. Some practical aspects for application of this technique are also discussed in this paper.

Think Twice: Effects on Diagnostic Accuracy of Returning to the Case to Reflect Upon the Initial Diagnosis.

Diagnostic errors have been attributed to failure to sufficiently reflect on initial diagnoses. However, evidence of the benefits of reflection is conflicting. This study examined whether reflection upon initial diagnoses on difficult cases improved diagnostic accuracy and whether reflection triggered by confrontation with case evidence was more beneficial than simply revising initial diagnoses. Participants were physicians in Bern, Switzerland, registered for the 2018 Swiss internal medicine certification exam. They diagnosed written clinical cases, providing an initial diagnosis by following the same instructions and returning to the case to provide a final diagnosis. The latter required different types of reflection depending on the physician's experimental condition: return without instructions, identify confirmatory evidence, identify contradictory evidence, or identify both confirmatory and contradictory evidence. The authors examined diagnostic accuracy scores (range 0-1) as a function of diagnostic phase and reflection type. One hundred and sixty-seven physicians participated. Diagnostic accuracy scores did not significantly differ between the 4 groups of physicians in the initial (I) or the final (F) diagnostic phase (mean [95% CI]: return without instructions, I: 0.21 [0.17, 0.26], F: 0.23 [0.18, 0.28]; confirmatory evidence, I: 0.24 [0.19, 0.29], F: 0.31 [0.25, 0.37]; contradictory evidence, I: 0.22 [0.17, 0.26], F: 0.26 [0.22, 0.30]; confirmatory and contradictory evidence, I: 0.19 [0.15, 0.23], F: 0.25 [0.20, 0.31]). Regardless of type of reflection employed while revising the case, accuracy increased significantly between initial and final diagnosis, I: 0.22 (0.19, 0.24) vs F: 0.26 (0.24, 0.29); P < .001. Physicians' diagnostic accuracy improved after reflecting upon initial diagnoses provided for difficult cases, independently of the evidence searched for while reflecting. The findings support the importance attributed to reflection in clinical teaching. Future research should investigate whether revising the case can become more beneficial by triggering additional reflection.

A Unified Description of Intrinsically Disordered Protein Dynamics under Physiological Conditions Using NMR Spectroscopy.

Intrinsically disordered proteins (IDPs) are flexible biomolecules whose essential functions are defined by their dynamic nature. Nuclear magnetic resonance (NMR) spectroscopy is ideally suited to the investigation of this behavior at atomic resolution. NMR relaxation is increasingly used to detect conformational dynamics in free and bound forms of IDPs under conditions approaching physiological, although a general framework providing a quantitative interpretation of these exquisitely sensitive probes as a function of experimental conditions is still lacking. Here, measuring an extensive set of relaxation rates sampling multiple-time-scale dynamics over a broad range of crowding conditions, we develop and test an integrated analytical description that accurately portrays the motion of IDPs as a function of the intrinsic properties of the crowded molecular environment. In particular we observe a strong dependence of both short-range and long-range motional time scales of the protein on the friction of the solvent. This tight coupling between the dynamic behavior of the IDP and its environment allows us to develop analytical expressions for protein motions and NMR relaxation properties that can be accurately applied over a vast range of experimental conditions. This unified dynamic description provides new insight into the physical behavior of IDPs, extending our ability to quantitatively investigate their conformational dynamics under complex environmental conditions, and accurately predicting relaxation rates reporting on motions on time scales up to tens of nanoseconds, both in vitro and in cellulo.

Effect of experimental conditions on nano-indentation response of low density polyethylene (LDPE)

Nano-indentation is an interesting tool for analyzing nano-scale mechanical properties. The analysis of nano-mechanical properties as a function of experimental conditions is very critical for designing engineering components. In this study, nano-indentation experiments were performed by considering different values of amplitude (1, 5, 10 nm), frequency (11.2, 22.5, 45 Hz), strain rate (0.02, 0.05, 0.1, 0.2, 1 s−1), peak load (10, 30, 100 mN) and hold time (1, 3, 5, 10, 20, 50, 100 sec) to analyze their effect on the mechanical properties of LDPE. The results showed that the effect of amplitude and frequency on the nano-mechanical properties of LDPE were negligible. Load-displacement curves displayed a shift towards higher indentation depths along with a decrease in peak load from 20.6 to 14.8 mN by having a decrease in strain rate from 1 to 0.02 s−1. Elastic modulus and hardness values exhibited a decrease with an increase in hold time. Logarithmic creep model was used to fit the experimental data of creep as a function of holding time which showed good agreement (r2 ≥ 0.97) with the experimental values. Recommended holding times are also suggested to eliminate the creep and nose problem in order to achieve high accuracy in measurements.

Switch in Relative Stability between cis and trans 2-Butene on Pt(111) as a Function of Experimental Conditions: A Density Functional Theory Study

The adsorption of cis and trans 2-butenes on Pt(111) has been studied as a function of hydrogen coverage θH by means of calculations based on density functional theory (DFT) with the inclusion of dispersion forces. All hydrogen coverages have been considered, from 0 to 1.00 monolayer (ML). For each case, the di-σ and π adsorption geometries of the olefins have been compared at a surface coverage of θC4H8 = 0.11 ML. Calculations of the Gibbs free energies of these systems have identified the most stable 2-butene isomer (cis or trans) as a function of coverage, temperature, and pressure. In particular, focus was placed on two sets of conditions, namely, one with a pressure of 10–7 Torr, a temperature of 80 K, and a gas ratio (PH2/Pbutene) of 25, similar to the conditions used in surface-science studies, and a second with a pressure of 1 bar, a temperature range of 300–400 K, and a gas ratio (PH2/Pbutene) of 10, similar to catalytic hydrogenation conditions. With all selected functionals (PW91, PBE-TS, and optPBE), di-σ bonding was found to be the most stable for both isomers of 2-butene and for all hydrogen coverages except for θH = 1.00 ML. At low pressures, 2-butene is physisorbed at low temperatures (≤125 K with PBE-TS and ≤90 K with optPBE); however, when the temperature increases, coadsorption of the butene with 6 H atoms becomes the most stable configuration of the system (θH = 0.67 ML), and finally, 2-butene desorbs around 380 K, as estimated with PBE-TS (or around 325 K with optPBE). Interestingly, a switch in stability was observed with hydrogen coverage, from the adsorbed trans isomer being the more stable for θH < 0.44 ML to the adsorbed cis isomer becoming the more stable at higher hydrogen coverages, in agreement with the cis–trans isomerization behavior previously reported for this system. At high pressures, the behavior is similar, but with transitions occurring at higher temperatures. 2-Butene is physisorbed until the temperature reaches 250 K, and desorbs above 500 K. At hydrogenation reaction temperatures (between 300 and 500 K), a hydrogen coverage of roughly half a monolayer was calculated (0.66 and 0.44 for 300 and 500 K, respectively). Our results confirm that dispersion effects must be included to properly describe the 2-butene and hydrogen coadsorption on Pt(111), as PW91 predicts that 2-butene is never adsorbed on the platinum surface. On the other hand, DFT calculations including dispersion forces such as PBE-TS or optPBE afford a good understanding of catalytic systems under both ultra-high-vacuum conditions and catalytic hydrogenation conditions. For this system, the PBE-TS results are in good agreement with experiments: they correctly reproduce the coverage in hydrogen and the configuration of the 2-butene adsorbate (cis–trans isomer).

Reactions of Organic Peroxides with Alcohols in Atmospheric Pressure Chemical Ionization-the Pitfalls of Quantifying Triacetone Triperoxide (TATP).

Over the last several decades, mass spectrometry has become one of the principle methods for compound identification and quantification. While for analytical purposes, fragments which are not fully characterized in terms of origin and intensity as a function of experimental conditions have been used, understanding the nature of those species is very important. Herein we discuss such issues relative to triacetone triperoxide (TATP) and its frequently observed fragment at m/z 89. This "fragment" has been identified as the gas-phase reaction product of TATP with one or two methanol molecules/ions. Additionally, the origin and conditions of other fragments at m/z 91, 75, and 74 associated with TATP will be addressed. Similar analytical issues associated with other multi-peroxide organic compounds [hexamethylene triperoxide diamine (HMTD), methyl ethyl ketone peroxides (MEKP)] will also be discussed. Solution storage conditions for TATP, HMTD, and tetramethylene diperoxide diamine dialdehyde have been determined. Graphical Abstract ᅟ.

Expression stability and selection of optimal reference genes for gene expression normalization in early life stage rainbow trout exposed to cadmium and copper

Gene expression analysis represents a powerful approach to characterize the specific mechanisms by which contaminants interact with organisms. One of the key considerations when conducting gene expression analyses using quantitative real-time reverse transcription-polymerase chain reaction (qPCR) is the selection of appropriate reference genes, which is often overlooked. Specifically, to reach meaningful conclusions when using relative quantification approaches, expression levels of reference genes must be highly stable and cannot vary as a function of experimental conditions. However, to date, information on the stability of commonly used reference genes across developmental stages, tissues and after exposure to contaminants such as metals is lacking for many vertebrate species including teleost fish. Therefore, in this study, we assessed the stability of expression of 8 reference gene candidates in the gills and skin of three different early life-stages of rainbow trout after acute exposure (24h) to two metals, cadmium (Cd) and copper (Cu) using qPCR. Candidate housekeeping genes were: beta actin (b-actin), DNA directed RNA polymerase II subunit I (DRP2), elongation factor-1 alpha (EF1a), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), glucose-6-phosphate dehydrogenase (G6PD), hypoxanthine phosphoribosyltransferase (HPRT), ribosomal protein L8 (RPL8), and 18S ribosomal RNA (18S). Four algorithms, geNorm, NormFinder, BestKeeper, and the comparative ΔCt method were employed to systematically evaluate the expression stability of these candidate genes under control and exposed conditions as well as across three different life-stages. Finally, stability of genes was ranked by taking geometric means of the ranks established by the different methods. Stability of reference genes was ranked in the following order (from lower to higher stability): HPRT<GAPDH<EF1a<G6PD<RPL8<DRP2<b-actin in gills of fish exposed to Cd; b-actin<GAPDH<G6PD<DRP2<RPL8<HPRT<EF1a in gills of fish exposed to Cu; RPL8<HPRT<GAPDH<G6PD<EF1a<DRP2<b-actin in the skin of fish exposed to Cd; and EF1a<GAPDH<RPL8<HPRT<G6PD<b-actin<DRP2 in the skin of fish exposed to Cu. The results demonstrated that the stability of reference genes depended on the metal, life-stage and/or organ in question. Thus, attention should be paid to these factors before selection of reference gene for relative quantification of the gene expressions.

Job perceptions following statewide evidence-based treatment implementation

PurposeThe concerns that implementing a new structured innovation with increased oversight may lead to reduced job autonomy and poorer work attitudes. These concerns have been cited as a barrier to evidence-based treatment (EBT) implementation. However, previous research found lower turnover among child welfare providers implementing an EBT with fidelity monitoring compared to those administering services as usual (SAU). The authors hypothesized that changes in job autonomy, job satisfaction, and organizational commitment would be no worse among providers in EBT conditions and fidelity monitoring conditions compared to SAU and no monitoring conditions.Design/methodology/approachSurvey data were collected from 208 service providers over four waves at six month intervals as part of a 2 (EBT vs SAU) by 2 (fidelity monitoring vs no monitoring) hybrid effectiveness-implementation trial. Superiority testing was conducted to determine whether there were significant differences over time on the outcomes as a function of experimental condition. Non-inferiority testing examined whether the EBT condition is not inferior to SAU and monitoring not inferior to no monitoring on the outcomes.FindingsNo evidence of superiority was found for any conditions over time on the outcomes. Non-inferiority testing indicates EBT is not inferior to SAU and monitoring is not inferior to no monitoring on the outcomes.Originality/valueThis study provide empirical quantitative data regarding job attitudes and job autonomy perceptions over time following EBT implementation. In light of the current findings, concerns regarding the impact of EBT implementation on provider job perceptions should be minimized.

Effect of pH, ionic strength, humic substances and temperature on the sorption of Th(IV) onto NKF-6 zeolite

Sorption of Th(IV) from aqueous solution to NKF-6 zeolite as a function of experimental conditions were investigated using batch experiments. The sorption of Th(IV) on NKF-6 zeolite was strongly dependent on pH and ionic strength at pH 6.0. The sorption of Th(IV) on NKF-6 zeolite was mainly dominated by ion exchange or outer-sphere surface complexation at low pH, while by inner-sphere surface complexation at high pH values. The thermodynamic data suggested that the sorption of Th(IV) on NKF-6 zeolite was an spontaneous and endothermic process. The results show that NKF-6 zeolite is a suitable adsorbent for Th(IV) enrichment from large amount of actual effluent.

Effect of solution chemistry on the interaction of radionuclide 63Ni(II) onto montmorillonite

Sorption of 63Ni(II) from aqueous solution to montmorillonite as a function of experimental conditions was studied, and the results indicated that the sorption of 63Ni(II) was mainly dominated by ion exchange or outer-sphere surface complexation at low pH, and by inner-sphere surface complexation or surface (co)precipitation at high pH. The presence of different cations had different influences on 63Ni(II) sorption, whereas the presence of different anions had no drastic influences on 63Ni(II) sorption. The thermodynamic parameters indicated that the sorption of 63Ni(II) on the montmorillonite was an endothermic and spontaneous process.

Machine learning assembly landscapes from particle tracking data.

Bottom-up self-assembly offers a powerful route for the fabrication of novel structural and functional materials. Rational engineering of self-assembling systems requires understanding of the accessible aggregation states and the structural assembly pathways. In this work, we apply nonlinear machine learning to experimental particle tracking data to infer low-dimensional assembly landscapes mapping the morphology, stability, and assembly pathways of accessible aggregates as a function of experimental conditions. To the best of our knowledge, this represents the first time that collective order parameters and assembly landscapes have been inferred directly from experimental data. We apply this technique to the nonequilibrium self-assembly of metallodielectric Janus colloids in an oscillating electric field, and quantify the impact of field strength, oscillation frequency, and salt concentration on the dominant assembly pathways and terminal aggregates. This combined computational and experimental framework furnishes new understanding of self-assembling systems, and quantitatively informs rational engineering of experimental conditions to drive assembly along desired aggregation pathways.

Single-Molecule Approaches for the Characterization of Riboswitch Folding Mechanisms.

Riboswitches are highly structured RNA molecules that control genetic expression by altering their structure as a function of metabolite binding. Accumulating evidence suggests that riboswitch structures are highly dynamic and perform conformational exchange between structural states that are important for the outcome of genetic regulation. To understand how ligand binding influences the folding of riboswitches, it is important to monitor in real time the riboswitch folding pathway as a function of experimental conditions. Single-molecule FRET (sm-FRET) is unique among biophysical techniques to study riboswitch conformational changes as it allows to both monitor steady-state populations of riboswitch conformers and associated interconversion dynamics. Since FRET fluorophores can be attached to virtually any nucleotide position, FRET assays can be adapted to monitor specific conformational changes, thus enabling to deduce complex riboswitch folding pathways. Herein, we show how to employ sm-FRET to study the folding pathway of the S-adenosylmethionine (SAM) and how this can be used to understand very specific conformational changes that are at the heart of riboswitch regulation mechanism.

Varying experimental conditions to study interactions in the solid state

Supramolecular interactions in the solid state attract much attention. Different experimental and computational approaches are used, to predict and to design crystal structures, to predict the properties based on molecular and crystal structures, to range different types of intermolecular interactions. Analysis of the crystal structures at fixed (e.g. ambient) temperature and pressure conditions is most common for experiments, whereas most DFT calculations are limited to 0 K, to minimize computational costs. At the same time, evolution of a crystal structure as a function of experimental conditions can contribute significantly to understanding the structure-forming role and relative energies of different types of intermolecular interactions in the same crystal structure and of similar interactions in a series of different but structurally or chemically related compounds. In the present invited contribution I attempt to illustrate this using several selected examples from my own practice and from the papers published by other research groups. I consider, in particular, the results of variable-temperature and variable-pressure studies of continuous lattice strain and phase transitions in small-molecule organic compounds, the results of variable-temperature and variable-pressure crystallization, the results of comparing the dissolution profiles of mono- and multi-component small-molecule organic crystals. I shall also discuss how variable-temperature and variable-pressure experimental diffraction data can assist in optimizing the calculations aimed at comparing the relative stability of polymorphs and predicting polymorph transitions. The study was supported by Russian Ministry of Science and Education and Russian Academy of Sciences.