Conformational Order Research Articles

Structural determination of model phospholipid membranes by Raman spectroscopy: Laboratory experiment.

In an upper-division interdisciplinary laboratory experiment, students use Raman spectroscopy to highlight how the overall structure and conformational order of lipid bilayers can be influenced by their individual phospholipid composition. Students prepare a supported lipid bilayer, as a model cell membrane, by spreading liposomes made of various phospholipids on a solid support. The characterization of phospholipid bilayers, a major component of cellular membranes, can advance our fundamental understanding of important biological phenomena, with significant implications in various fields including drug delivery and development. We use Raman spectroscopy as an analytical tool to investigate the structural and packing properties of model cell membranes. The spectral frequency, intensity, and line-width of lipid Raman bands are extremely sensitive to structural alterations. This experimental module effectively exposes students to the fundamentals of Raman spectroscopy and teaches students the importance of interdisciplinary education as they integrate concepts from chemical structure, molecular interactions, and analytical spectroscopic techniques to gain a more holistic understanding of biological membrane properties.

Reclined trend of alkyl chain of sodium dodecylbenzenesulfonate molecules induced by friction

Surfactants tend to adsorb on the surface/interface mostly in a directional manner. The alkyl chain orientation and conformation order for molecular monolayers of sodium dodecylbenzenesulfonate (SDBS) at low concentrations are studied by using the sum frequency generation vibrational spectroscopy (SFG-VS). The molecular arrangement of the surfactants adsorbed at the solid/liquid interface is further investigated. It is found that the arrangement of the SDBS at the interface becomes relatively ordered with increasing bulk concentration. Meanwhile, the orientation angle reduces gradually, and the molecules tend to be upright state. In addition, the effect of friction on the conformation order and orientation angle are also analyzed. The intensity of the SDBS vibrational contraction peak becomes lower after friction, which indicates that the anion has a reorientation process at the interface. The arrangement of molecules becomes more disordered due to friction. The orientation angle increases slightly, which indicates the monolayer has an inclined trend relative to the lateral direction on the interface. A modified adsorption model considering friction effect is proposed. This work may provide a reference for the further study of adsorption mechanism and application of surfactants.

Mathematical Modeling of Coronavirus Dynamics with Conformable Derivative in Liouville–Caputo Sense

Coronavirus has become a serious global phenomenon in recent times and has negative effects on the entire world economy. In this study, a fractional mathematical model formulated in fractional conformable derivative is studied. The model hinges on the concept of mammal hosts and humans. The basic properties of the coronavirus model are investigated. The stability analysis is carried out as well as sensitivity analysis based on the reproduction number. Numerical simulation is undertaken to give impetus to the analytical results which indicate that both fractional conformable order derivative and fractional‐order derivative have serious consequences in numerical result outcomes.

Conformational dynamics promotes disordered regions from function-dispensable to essential in evolved site-specific DNA recombinases

Protein intrinsically disordered regions (IDRs) play pivotal roles in molecular recognition and regulatory processes through structural disorder-to-order transitions. To understand and exploit the distinctive functional implications of IDRs and to unravel the underlying molecular mechanisms, structural disorder-to-function relationships need to be deciphered. The DNA site-specific recombinase system Cre/loxP represents an attractive model to investigate functional molecular mechanisms of IDRs. Cre contains a functionally dispensable disordered N-terminal tail, which becomes indispensable in the evolved Tre/loxLTR recombinase system. The difficulty to experimentally obtain structural information about this tail has so far precluded any mechanistic study on its involvement in DNA recombination. Here, we use in vitro and in silico evolution data, conformational dynamics, AI-based folding simulations, thermodynamic stability calculations, mutagenesis and DNA recombination assays to investigate how evolution and the dynamic behavior of this IDR may determine distinct functional properties. Our studies suggest that partial conformational order in the N-terminal tail of Tre recombinase and its packing to a conserved hydrophobic surface on the protein provide thermodynamic stability. Based on our results, we propose a link between protein stability and function, offering new plausible atom-detailed mechanistic insights into disorder-function relationships. Our work highlights the potential of N-terminal tails to be exploited for regulation of the activity of Cre-like tyrosine-type SSRs, which merits future investigations and could be of relevance in future rational engineering for their use in biotechnology and genomic medicine.

Size and surface coverage density are major factors in determining thiol modified gold nanoparticles characteristics

Gold nanoparticles (GNPs) have prominent advantages due to their ultrasmall size and high surface-area-to-volume ratio, with multiple and broad applications in medical, agricultural and pharmaceutical industries. GNPs can be functionalized by various molecules including polysaccharides, proteins, peptides, fatty acids, plasmids, or oligonucleotides. GNP surface represents one of the most easily functionalized platforms, the complex level of surface decoration being used to obtain efficacy and to limit off-target toxicity. In the present study, molecular dynamics simulations of thiol modified GNPs were performed to provide insights at the molecular level for the design of conjugated nanoparticles. Our study shows that due to the significant enhancement in the conformational order and packing of the thiol chains, both nanoparticle size and thiol coverage density can be used to modify the structural properties of thiol-modified GNPs (e.g. end-to-end distance, shape factor, tilt angle of thiol chains). This strategy has a lot of potential in designing any (thiol-modified gold) nanoparticle-based carriers (such as those that are used to find and modify the genes that are associated with diseases).

Conformational Order of Alkyl Side Chain of Poly(3-alkylthiophene) Promotes Hole-Extraction Ability in Perovskite/Poly(3-alkylthiophene) Heterojunction.

Molecular structures of hole transport materials (HTMs) have significant impact on the optoelectronic properties of perovskite/HTM heterojunction. But the structure-property relationship in the heterojunction remains poorly understood. By using poly(3-alkylthiophene) (P3AT) as the HTM model, here we apply sum frequency generation vibrational spectroscopy to establish correlations among conformations of P3ATs, the hole extraction ability of P3ATs from the perovskite layer, and the charge mobility of P3ATs. It is revealed that with similar energy-level alignment, the conformational order of alkyl side chains in regioregular P3ATs can effectively regulate the hole extraction ability of P3ATs from perovskite layer by tuning reorganization energy. By contrast, the charge mobility of P3ATs strongly depends on the P3AT backbone's coplanarity. Our findings decouple the roles of the long-hidden conformational order of alkyl side chain and the polythiophene backbone's coplanarity on the performance of perovskite/HTM heterojunction, offering useful guidelines for boosting the performance of optoelectronic devices.

Modeling and numerical investigation of a conformable co‐infection model for describing Hantavirus of the European moles

The aim of this work is to investigate theoretically and numerically a conformable‐order epidemiological model of the Susceptible‐Infected (SI) type. The qualitative properties of the solutions are studied. Besides, the dynamics of the problem is discussed in detail. The conformable version of the implicit and explicit Adams multistep methods is proposed with the formulation of the truncation error. An inverse optimization problem using the least square method is introduced to estimate the model parameters. Moreover, to show the effectiveness of the conformable order in describing the studied phenomena and to calibrate the model, some created data of Nova and Bruges virus in Belgium were used.

Dynamic response on a nanometer scale of binary phospholipid-cholesterol vesicles: Low-frequency Raman scattering insight.

Low-frequency Raman spectroscopy was used to study the dynamic response on a nanometer scale of aqueous suspensions of two-component lipid vesicles. Binary mixtures of saturated phospholipid (1,2-dipalmitoyl-sn-glycero-3-phosphocholine, DPPC) and cholesterol are interesting for possible coexistence of solidlike and liquid-ordered phases, while the phase coexistence was not reported for unsaturated phospholipid (1,2-dioleoyl-sn-glycero-3-phosphocholine, DOPC) and cholesterol mixtures. The DOPC-DPPC mixtures represent the well-documented case of coexisting domains of solidlike and liquid-disordered phases. These three series of lipid mixtures are studied here. A broad peak with the maximum in the range of 30-50cm^{-1} and a narrow peak near 10cm^{-1} are observed in the Raman susceptibility of the binary mixtures and attributed to the acousticlike vibrational density of states and layer modes, respectively. Parameters of the broad and narrow peaks are sensitive to lateral and conformational hydrocarbon chain ordering. It was also demonstrated that the low-frequency Raman susceptibility of multicomponent lipid bilayers allows one to determine the phase state of lipid bilayers and distinguish the homogeneous distribution of molecular complexes from coexisting domains with sizes above several nanometers. Thus, the low-frequency Raman spectroscopy provides unique information in studying phase coexistence in lipid bilayers.

Raman scattering in protonated and deuterated 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine (DPPC): Indicators of conformational and lateral orders

The use of deuterocarbons is an effective method in the Raman spectroscopy of multicomponent lipid materials and biological samples. Here, Raman spectra of hydrated multilamellar vesicles of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), its deuterated analog 1,2-dipalmitoyl-d62-sn-glycero-3-phosphocholine (DPPCd62), and DPPC-DPPCd62 mixtures were studied in a wide temperature range to specify the Raman indicators of conformational and lateral orders. The temperature dependence of the 985 cm−1 line in the deuterated phospholipid unequivocally indicates that this line corresponds to the CC stretching vibrations of deuterated hydrocarbon chains in the all-trans conformation. It was also concluded that the ratio of Raman intensities at the maximum of the peak of the symmetric CD2 stretching and at a maximum near 2168 cm−1 reflects the conformational order of the hydrocarbon chain and can be used for an evaluation of the fraction of the all-trans sequences. The frequency of the symmetric CD2 stretching peak is sensitive to the phase state (gel or fluid) but has a low sensitivity to the partial conformational disordering within the gel phase. The Raman study of DPPC-DPPCd62 mixtures reveals that the lateral order contributes to the ratio of intensities of the antisymmetric and symmetric CH2 stretching peaks as a prefactor enhancing the effect of conformational ordering.

Research on Population Development Trend in Huizhou of China Forecast Based on Optimal Weighted Combination Method and Fractional Grey Model

In this paper, the optimal weighted combination model and fractional grey model are constructed. The coefficients of the optimal weighted combination model are determined by minimizing the sum of squares of resists of each model. On the other hand, the optimal conformable fractional order and dynamic background value coefficient are determined by the quantum inspired evolutionary algorithm (QIEA). Taking the resident population from 2008 to 2018 as the research object, the optimal weighted combination model and fractional grey model were used to study the estimated and predicted values. The results are compared and analyzed. The results show that the fractional grey model is better than the optimal weighted combination model in the estimation of the values. The optimal weighted combination model is better than the fractional grey model in predicting. Meanwhile, the fractional grey model is found to be very suitable for the data values that are large, and the changes between the data are relatively small. The research results expand the application of the fractional grey model and have important implications for the policy implementation activities of Huizhou government according to the population growth trend in Huizhou.

Compactified holographic conformal order

We study holographic conformal order compactified on S3. The corresponding boundary CFT4 has a thermal phase with a nonzero expectation value of a certain operator. The gravitational dual to the ordered phase is represented by a black hole in asymptotically AdS5 that violates the no-hair theorem. While the compactification does not destroy the ordered phase, it does not cure its perturbative instability: we identify the scalar channel QNM of the hairy black hole with Im[w]>0. On the contrary, we argue that the disordered thermal phase of the boundary CFT is perturbatively stable in holographic models of Einstein gravity and scalars.

Iterative learning control for fractional order nonlinear system with initial shift

In this study, a closed-loop \({D^\alpha }\)-type iterative learning control (ILC) with a proportional D-type iterative learning updating law for the initial shift is applied to nonlinear conformable fractional order system. First, the system with the initial shift is introduced. Then, fractional order ILC (FOILC) frameworks that experience the initial shift problem for the path tracking of nonlinear conformable fractional order systems are addressed. Moreover, the sufficient condition for the convergence of tracking errors is obtained in the time domain by introducing \(\lambda \)-norm and Hölder’s inequality. Lastly, numerical examples are provided to illustrate the effectiveness of the proposed methods.

Correlations among the Raman spectra and the conformational compositions of ethylene glycol, 1,2- and 1,3-propylene glycols

• Raman bands about 800 cm -1 are markers of conformational compositions of the diols. • Experiments and DFT calculations show prevalence of gauche conformers for the diols. • The gas-phase approximation does not describe fully Raman spectra of the liquid diols. • DFT spectra of molecular clusters match well experimental spectra of liquid EG. • Intermolecular interactions lead to significant distortion of molecular conformations. Raman spectra of liquid ethylene glycol (EG), 1,2-propylene glycol (1,2-PG) and 1,3-propylene glycol (1,3-PG) were analyzed in terms of the conformational composition of the molecules. The analysis was based on comparison of the experimental spectra with the results of the density functional theory (DFT) calculations of the structure, energy and Raman spectra for 10 conformations of EG molecule, 27 conformations of 1,2-PG molecule and 25 conformations of 1,3-PG molecule. The gas-phase approximation calculations well describe the main features of the experimental spectra of the liquid substances in the region 600 – 1600 cm −1 . Calculations for clusters of EG molecules showed that an increase in the number of molecules in a cluster leads to significant improvement of the agreement between the calculated and experimental spectra. The conformations of molecules in the clusters are strongly distorted in comparison with the results of the gas-phase approximation. Thus, the intermolecular interactions influence significantly the conformational order and the Raman spectra of the diols.

Bipolar Imidazolium-Based Lipid Analogues for Artificial Archaeosomes.

Archaeal lipids have harvested biomedical and biotechnological interest because of their ability to form membranes with low permeability and enhanced temperature and pressure stability. Because of problems in isolating archaeal lipids, chemical synthesis appears to be a suitable means of producing model lipids that mimic the biological counterparts. Here, we introduce a new concept: we synthesized bipolar alkylated imidazolium salts of different chain lengths (BIm10-32) and studied their structure and lyotropic phase behavior. Furthermore, mixtures of the bolalipid analogues with phospholipid model biomembranes of diverse complexity were studied. DSC, fluorescence and FTIR spectroscopy, confocal fluorescence microscopy, DLS, SAXS, and TEM were used to reveal changes in lipid phase behavior, fluidity, the lipid's conformational order, and membrane morphology over a wide range of temperatures and for selected pressures. It could be shown that the long-chain BImN32 can form monolayer sheets. Integrated in phospholipid membranes, it reveals a fluidizing effect. Here, the two polar head groups, connected by a long alkyl chain, enable the integration into the bilayer. Interestingly, addition of BImN32 to fluid DPPC liposomes increased the lipid packing markedly, rendering the membrane system more stable at higher temperatures. The membrane system is also stable against compression as indicated by the high-pressure stability of the system, mimicking an archaeal lipid-like behavior. BImN32 incorporation into raft-like anionic model biomembranes led to marked changes in lateral membrane organization, topology, and fusogenicity of the membrane. Overall, it was found that long-chain imidazolium-based bolalipid analogues can help adjust membrane's biophysical properties, while the imidazolium headgroup provides the ability for crucial electrostatic interaction for vesicle fusion or selective interaction with membrane-related signaling molecules and polypeptides in a synthetically tractable manner. The results obtained may help to develop new approaches for rational design of extremophilic bolalipid-based liposomes for various applications, including delivery of drugs and vaccines.

Conformational Freedom‐Enhanced Optomechanical Energy Conversion Efficiency in Bulk Azo‐Polyimides

AbstractAzobenzene‐doped glassy polyimides (azo‐polyimides) offer some of the most efficient optomechanical power densities to date rivaling electrostrictive polymers. Despite such potential attributes, the optomechanical efficiency remains low in comparison to other smart materials. Using high‐fidelity coarse‐grained molecular dynamics simulations, the authors reconcile both experimental and theoretical challenges to understand the limiting factors for the optomechanical conversion in photostrictive polymers. Interestingly, the ideal optomechanical efficiency of 10–24% for a single‐chain azo‐imide monomer predicted here is equal to or a little higher than experimental reports, suggesting experimental design space. The time‐dependent optomechanical efficiency of bulk azo‐polyimide is quantified, for the first time, to be strongly correlated with the initial free volumes, a measure of polymer conformational freedom. This trend is elaborated by conformational order parameters and viscoelastic relaxation moduli. Resembling the role of porosity in azobenzene‐contained metal/covalent organic frameworks to enhance the photo‐switching efficiency, a larger conformational freedom enables >10 times increase in optomechanical efficiency comparing to existing experiments. This is primarily due to facilitated viscoelastic relaxation after photo‐switching which alleviates residual stresses quickly and reduces heat dissipation. These findings suggest opportunities to improve the optomechanical performance through targeted strategies, such as porosity control and thermal annealing.

Fractional numerical dynamics for the logistic population growth model under Conformable Caputo: a case study with real observations

Models of population dynamics are substantially non-Markovian in nature and exhibit behavior for memory effects. This research study investigates the logistic growth model from population dynamics under both classical and non-classical (fractional) differential operators using actual statistical data. For the non-classical differential operator, the operator called conformable fractional derivative having order β in the sense of Liouville-Caputo (LC) of order α is employed while taking care of its dimensional consistency. Working parameters including conformable fractional derivative order β, LC having order α, growth rate ζ, and carrying capacity Φ have been optimized, and the results are compared with those of classical one. Error rate suggests the superiority of the fractional conformable logistic model whose solutions are investigated for uniqueness via fixed point theory. Numerical simulations using Adams' iterative technique recently proposed for the conformable fractional derivative are illustrated in figures for a thorough understanding of the model's behavior, along with a statistical summary for the operators. An attractive chaotic attractor is observed in the fractional logistic model when ζ ≥ 4.023. Cumulative effects of growth rate and carrying capacity on the population's change in the logistic model are also investigated with 3D graphics.

Potential Role of Plasmalogens in the Modulation of Biomembrane Morphology.

Plasmalogens are a subclass of cell membrane glycerophospholipids that typically include vinyl- ether bond at the sn-1 position and polyunsaturated fatty acid at the sn-2 position. They are highly abundant in the neuronal, immune, and cardiovascular cell membranes. Despite the abundance of plasmalogens in a plethora of cells, tissues, and organs, the role of plasmalogens remains unclear. Plasmalogens are required for the proper function of integral membrane proteins, lipid rafts, cell signaling, and differentiation. More importantly, plasmalogens play a crucial role in the cell as an endogenous antioxidant that protects the cell membrane components such as phospholipids, unsaturated fatty acids, and lipoproteins from oxidative stress. The incorporation of vinyl-ether linked with alkyl chains in phospholipids alter the physicochemical properties (e.g., the hydrophilicity of the headgroup), packing density, and conformational order of the phospholipids within the biomembranes. Thus, plasmalogens play a significant role in determining the physical and chemical properties of the biomembrane such as its fluidity, thickness, and lateral pressure of the biomembrane. Insights on the important structural and functional properties of plasmalogens may help us to understand the molecular mechanism of membrane transformation, vesicle formation, and vesicular fusion, especially at the synaptic vesicles where plasmalogens are rich and essential for neuronal function. Although many aspects of plasmalogen phospholipid involvement in membrane transformation identified through in vitro experiments and membrane mimic systems, remain to be confirmed in vivo, the compiled data show many intriguing properties of vinyl-ether bonded lipids that may play a significant role in the structural and morphological changes of the biomembranes. In this review, we present the current limited knowledge of the emerging potential role of plasmalogens as a modulator of the biomembrane morphology.

Newton’s Law of Cooling with Generalized Conformable Derivatives

In this communication, using a generalized conformable differential operator, a simulation of the well-known Newton’s law of cooling is made. In particular, we use the conformable t1−α, e(1−α)t and non-conformable t−α kernels. The analytical solution for each kernel is given in terms of the conformable order derivative 0<α≤1. Then, the method for inverse problem solving, using Bayesian estimation with real temperature data to calculate the parameters of interest, is applied. It is shown that these conformable approaches have an advantage with respect to ordinary derivatives.

Sürekli Mıknatıslı Senkron Motorun Hız Takip Sistemi için Uygun Kesirli PI Kontrolör Tasarımı ve Optimizasyonu

The use of permanent magnet synchronous motor (PMSM) is increasing rapidly to meet the need to increase efficiency in variable speed drive systems used in the industry, in recent years. This paper aims to improve the speed control performance of the PMSM based systems. To achieve this, a PMSM speed controller is designed based on the conformable fractional order proportional integral (CFOPI) method. CFOPI controller coefficients kp, ki and γ are optimized using response surface method (RSM). To validate the success of the proposed scheme, the CFOPI controller and the integer order PI (IOPI) controller are tested under the same simulation model and the results are compared. The proposed method grants robust performance with less computational load then the classical fractional order controllers for variable referenced PMSM speed tracking systems. The CFOPI controller can be applied easily for industrial variable speed drive systems which is using PMSM to improve the performance and stability of the systems.

Conformer-dependent vacuum ultraviolet photodynamics and chiral asymmetries in pure enantiomers of gas phase proline

Proline is a unique amino-acid, with a secondary amine fixed within a pyrrolidine ring providing specific structural properties to proline-rich biopolymers. Gas-phase proline possesses four main H-bond stabilized conformers differing by the ring puckering and carboxylic acid orientation. The latter defines two classes of conformation, whose large ionization energy difference allows a unique conformer-class tagging via electron spectroscopy. Photoelectron circular dichroism (PECD) is an intense chiroptical effect sensitive to molecular structures, hence theorized to be highly conformation-dependent. Here, we present experimental evidence of an intense and striking conformer-specific PECD, measured in the vacuum ultraviolet (VUV) photoionization of proline, as well as a conformer-dependent cation fragmentation behavior. This finding, combined with theoretical modeling, allows a refinement of the conformational landscape and energetic ordering, that proves inaccessible to current molecular electronic structure calculations. Additionally, astrochemical implications regarding a possible link of PECD to the origin of life’s homochirality are considered in terms of plausible temperature constraints.