Dynamic Properties Research Articles

ModXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields.

Modified nucleic acids have surged as a popular therapeutic route, emphasizing the importance of nucleic acid research in drug discovery and development. Beyond well-known RNA vaccines, antisense oligonucleotides and aptamers can incorporate various modified nucleic acids to target specific biomolecules for various therapeutic activities. Molecular dynamics simulations can accelerate the design and development of these systems with noncanonical nucleic acids by observing intricate dynamic properties and relative stability on the all-atom level. However, modeling these modified systems is challenging due to the time and resources required to parametrize components outside default force field parameters. Here, we present modXNA, a tool to derive and build modified nucleotides for use with Amber force fields. Several nucleic acid systems varying in size and number of modification sites were used to evaluate the accuracy of modXNA parameters, and results indicate the dynamics and structure are preserved throughout the simulations. We detail the protocol for quantum mechanics charge derivation and describe a workflow for implementing modXNA in Amber molecular dynamics simulations, which includes updates and added features to CPPTRAJ.

Unraveling the molecular determinants of a rare human mitochondrial disorder caused by the P144L mutation of FDX2.

Episodic mitochondrial myopathy with or without optic atrophy and reversible leukoencephalopathy (MEOAL) is a rare, orphan autosomal recessive disorder caused by mutations in ferredoxin-2 (FDX2), which is a [2Fe-2S] cluster-binding protein participating in the formation of iron-sulfur clusters in mitochondria. In this biosynthetic pathway, FDX2 works as electron donor to promote the assembly of both [2Fe-2S] and [4Fe-4S] clusters. A recently identified missense mutation of MEOAL is the homozygous mutation c.431C>T (p.P144L) described in six patients from two unrelated families. This mutation alters a highly conserved proline residue located in a loop of FDX2 that is distant from the [2Fe-2S] cluster. How this Pro to Leu substitution damages iron-sulfur cluster biosynthesis is unknown. In this work, we have first compared the structural, dynamic, cluster binding and redox properties of WT and P144L [2Fe-2S] FDX2 to have clues on how the pathogenic P144L mutation can perturb the FDX2 function. Then, we have investigated the interaction of both WT and P144L [2Fe-2S] FDX2 with its physiological electron donor, ferredoxin reductase FDXR, comparing their electron transfer efficiency and protein-protein recognition patterns. Overall, the data indicate that the pathogenic P144L mutation negatively affects the FDXR-dependent electron transfer pathway from NADPH to FDX2, thereby reducing the capacity of FDX2 in assembling both [2Fe-2S] and [4Fe-4S] clusters. Our study also provided solid molecular evidences on the functional role of the C-terminal tail of FDX2 in the electron transfer between FDX2 and FDXR.

Effect of Non-Uniform Temperature Distribution on the Natural Frequency of Concrete Girder Bridges

Structural dynamic properties like frequencies and mode shapes have been widely adopted for bridge condition assessment and damage identification. One of the main challenges lies in environmental factors, particularly the varying temperature, which significantly influences the bridge’s natural frequencies. In some cases, the effect of temperature changes can be comparable to, or even exceed, the effect caused by damage, rendering the damage identification methods ineffective. This study investigates the influence of the cross-sectional non-uniform temperature distribution, as a result of surrounding environmental factors, on the frequency of concrete girder bridges. A theoretical analysis is conducted to derive the bridge’s frequencies considering the cross-sectional non-uniform temperature distribution. The upper and lower bounds of the frequencies are developed by using only the environmental temperature and the largest temperature gradient defined by codes. More importantly, the damage to the bridge can be detected if the frequencies exceed the bounds for a certain period. This approach is convenient and practical in real applications without embedding thermocouples in the main girder. Numerical simulations, laboratory experimental tests, and field measurements are carried out to validate the derived frequency considering the cross-sectional non-uniform temperature distribution as well as the upper and lower bounds of the frequency. In particular, the results of the Z24 bridge show that when the bridge is damaged, the measured frequency exceeds the bound continuously, verifying the capability of the developed upper and lower bounds to evaluate bridge conditions.

Experimental Investigation on the Mechanical and Dynamic Thermomechanical Properties of Polyether Ether Ketone Based on Fused Deposition Modeling

In this work, the mechanical and dynamic thermomechanical properties of PEEK based on FDM are experimentally investigated and evaluated comprehensively. The tensile failure mechanism of PEEK prepared by FDM and extrusion modeling (EM) was analyzed by fracture morphology observation. By conducting a differential scanning calorimetry (DSC) test, the crystallinity of PEEK prepared by FDM and EM was measured. The dynamic thermomechanical properties of PEEK were tested and analyzed by dynamic mechanical analysis (DMA). For FDM-prepared PEEK samples, the yield strength and elongation were 98.3 ± 0.49 MPa and 22.86 ± 2.12%, respectively. Compared with the yield strength of PEEK prepared by EM, the yield strength of PEEK prepared by FDM increased by 65.38%. The crystallinity of FDM-prepared and EM-prepared samples was calculated as 34.81% and 31.55%, respectively. Different processing methods resulted in differences in the microscopic morphology and crystallinity of two types of PEEK parts, leading to differences in mechanical properties. The internal micropores generated during the FDM processing of PEEK significantly reduced the elongation. Moreover, according to the DMA results, the glass transition activation energy of PEEK was obtained as ΔE = 685.07 kJ/mol based on the Arrhenius equation. Due to the excellent mechanical properties of PEEK prepared by FDM processing, it is promising for high-performance polymer applications in different fields.

Rich dynamics of a hepatitis C virus infection model with logistic proliferation and time delays

AbstractIn this paper, we study a dynamic model of hepatitis C virus (HCV) infection with density‐dependent proliferation of uninfected and infected hepatocytes and two time delays, which is derived from a three‐dimensional model by the quasi‐steady‐state approximation. The model can exhibit forward bifurcation or backward bifurcation, and an explicit control threshold parameter is obtained for the case of backward bifurcation. It is shown that if the proliferation rate of infected hepatocytes is greater than the proliferation rate of uninfected hepatocytes by a certain amount, it becomes more difficult for the virus to be removed. The model has rich dynamical properties: (i) In some parameter regions, bistability can occur; (ii) both time delays (virus‐to‐cell delay) and (cell‐to‐cell delay) can lead to Hopf bifurcations; (iii) same length of time delays and can lead to at most one stability switch, but different time delays can lead to multiple stability switches. Several sufficient conditions for the global stability of the disease‐free equilibrium and the endemic equilibrium are obtained for both forward and backward bifurcation scenarios. In particular, several sharp results on global stability are obtained. Theoretical and numerical results portray the complexity of viral evolutionary dynamics in chronic HCV‐infected patients.

Dynamic stability analysis of the aircraft electrical power system in the more electric aircraft concept

This paper presents the modelling and analysis process of the electrical power management system on board an electrified aircraft conforming to the More/All Electric Aircraft concept. The main objective of the study is to assess the stability of the Electric Power Distribution System under different operational conditions, including the aspect of constant power loads. The paper describes the structure of the system, in which the key role is played by a synchronous generator and a three-phase rectifier converting alternating current AC into direct current DC. To solve the problem, modeling methods in the Matlab/Simulink environment were used, which enabled the analysis of the dynamic properties of the system and the assessment of stability under various types of loads. The obtained test results show that the presence of constant power loads can lead to instability in the EPDS system, manifested by voltage and current oscillations exceeding the standards specified in the MIL-STD-704E standard. The paper also provides tools for predicting system stability without the need to conduct full stability tests, which is important for the design of modern aviation power systems. The final section of the work presents the research results obtained and the resulting significant insights and practical conclusions.

Differential postnatal cardiovascular course of donor-recipient twins and associated pathophysiology-a cohort study.

Fetal echocardiography in twin to twin transfusion pregnancies treated with photocoagulation noted impaired cardiac function. Systematic information about cardiac structure or function and arterial distensibility after birth is not available. This study evaluated cardiovascular function and arterial dynamic properties in survivors of twin to twin transfusion syndrome. Eleven pairs of donor-recipient twins were compared with each other, and with 20 singletons of comparable gestational age. The twin cohort was born at 31.5±2 weeks gestational age; birthweights of donors-recipients were comparable (donors: 1358±421g vs recipients: 1617±460g, P=0.2). Significant inter-twin differences were noted for cardiac function parameters. Recipients had greater septal thickness (donors: 2.3±0.15 vs recipients: 2.7±0.36mm, P=0.01) and globularity (lower sphericity index [donors: 1.76±0.1 vs recipients: 1.62±0.12, P=0.009]). They also had lower cardiac function (tricuspid annular plane systolic excursion [donors: 4.6±0.5 vs recipients: 4.1±0.4mm, P=0.02) and right ventricular fractional area change [donors: 30±1 vs recipients: 27.7±1.3%, P=0.0001]). Comparing with singletons, differences were statistically more significant for recipients. Arterial distensibility however, was more affected in donors (higher arterial wall stiffness index [donors: 2.5±0.2 vs recipients: 2.2±0.2, P=0.008] and lower pulsatile diameter [donors: 51±5 vs recipients: 63±10 µm, P<0.0001). Comparing with singletons, the differences were statistically more significant for donors. Evaluation in the neonatal period noted that cardiac function and arterial distensibility is affected in TTTS twins. These cohorts will benefit from close postnatal follow up for resolution of cardiac and arterial impairments.

Design and damping characterization of sandwich composite made of particle-filled hollow spheres and steel sheets

Sandwich composites made of particle-filled hollow sphere structures (PHSS) and steel sheets offer excellent lightweight and damping properties, ideal for high-speed machine tool components under dynamic loads. Previous research has focused on single particle-filled hollow sphere (PHS) and small PHSS, leaving a gap understanding of PHSS/steel sandwich composites. In this study a test rig was developed, and Design of Experiments and Response Surface Analysis were used to investigate the effects of sheet and core thickness (design parameters), filling ratio, and particle size (particle parameters) on the damping performance of PHSS/steel sandwiches. The results indicate that the design parameters have a significant influence on damping performance. The interaction between design and particle parameters also substantially affects damping. Minimizing particle size, increasing filling ratio, thinning the face layer, and thickening the core layer significantly improve structural damping. To address manufacturing tolerances, a finite element (FE) model-based optimization was developed to accurately determine PHSS material parameters. These parameters were used in an FE model of the PHSS-steel composite, with identified contact parameters minimizing measurement and simulation differences. The homogenized material model and the linear model using global damping parameters accurately reproduce the dynamic properties of the PHSS-steel sandwich composite in low vibration modes.

Impact of Various High Intensity Earthquake Characteristics on the Inelastic Seismic Response of Irregular Medium-Rise Buildings

In the twenty-first century, the seismic design of buildings seems to have become a fully recognized topic. There are guidelines and standards which should be taken into account by designers in seismic areas. Designers using modern international guidelines have ascertained that the behavior of structures is not as expected. New challenges in the construction industry result in the construction of structures with new, unusual shapes. These are structures that do not meet the assumptions of safe construction in seismic areas. Contemporary buildings are also characterized by their irregular distribution of structural elements. Such solutions are not beneficial from the point of view of seismic engineering and can lead to reduced dynamic resistance and damage in such structures. In this paper, a five-storey, irregular-shaped reinforced concrete (RC) building model was subjected to different earthquakes with varying magnitudes, PGA (peak ground acceleration) and PGV (peak ground velocity) values, and durations of the intense shock phase. Once the model was verified using previous in situ measurements, the building model was subjected to five earthquakes. A numerical nonlinear analysis of the building was performed using a verified FEA (finite element analysis) model in the time domain through non-linear time history analysis with the Broyden–Fletcher–Goldfarb–Shanno (BFGS) method. The building’s dynamic properties were measured using various methods of excitation. The model was influenced, among others, by two far-field representative events caused by the last earthquake in Turkey, which resulted in strong ground motion. The analysis results identified the locations of structural damage and allowed for the assessment of the structure’s dynamic resistance. The results of the calculations prove that the duration of the intensive phase of extortion is one of the reasons for building damage in earthquake-prone areas. Building damage occurs with earthquakes that are characterized by an intensive phase of excitation with a long duration and high values of velocity in the earthquake components. The article highlights the inadequate dynamic resistance of the building, leading to excessive displacements and unfavorable structural solutions. Damage to buildings at this earthquake intensity caused damage to the load-bearing structure, which was not designed for such intensities. This paper is a research report with a specific case study of medium-rise irregular RC buildings.

Transcendence and Normality of Complex Numbers via Hurwitz Continued Fractions

Abstract We study the topological, dynamical, and descriptive set-theoretic properties of Hurwitz continued fractions. Hurwitz continued fractions associate an infinite sequence of Gaussian integers to every complex number that is not a Gaussian rational. The resulting space of sequences of Gaussian integers $\Omega $ is not closed. Using an iterative procedure, we show that $\Omega $ contains a natural subset whose closure $\overline{\textsf{R}}$ encodes continued fraction expansions of complex numbers that are not Gaussian rationals. We prove that $(\overline{\textsf{R}}, \sigma )$ is a subshift with a feeble specification property. As an application, we determine the rank in the Borel hierarchy of the set of Hurwitz normal numbers with respect to the complex Gauss measure. We also construct a family of complex transcendental numbers with bounded partial quotients.

Nonstructure–structure interaction with respect to mass ratio: Numerical analysis and free vibration tests

The dynamic interactions between nonstructural components (NCs) and the main building structure cannot be neglected because the dynamic properties of the main structure are modified, particularly for heavy NCs. The mass ratio (MR) is a parameter that incorporates the nonstructure–structure interaction (NSI) between the NCs and main structure. In this study, to investigate the seismic interaction in terms of the MR, a four-story steel moment frame was constructed and free vibration tests were carried out. The equivalent mass of the NCs was connected to various floor levels, neglecting their stiffness and damping. The vibration mode and period of the steel frame were obtained numerically. At MR = 25 %, the period generally increased with increasing MR. The modal contribution factors in terms of the roof displacement and base shear were analyzed. The findings show that it would be safe to consider the 1st mode only when using the roof displacement, whereas more modes should be considered when the base shear is used. The experimental damping ratios correlated with the magnitude of the MR without a representative trend. The damping ratio generally increases with an increase in the number of floors hosting additional masses. The experimental period increased almost linearly with the MR irrespective of the number of floor-hosting masses. An equivalent single-degree-of-freedom model is developed to predict the frame period. The predicted periods generally matched the experimental results. The normalized height of the equivalent model and period ratio vary with the MR and are correlated with the number of floors hosting the mass. The results of this study will be beneficial for the seismic design of building structures with heavy NCs.

Interaction of lump, periodic, bright and kink soliton solutions of the (1+1)-dimensional Boussinesq equation using Hirota-bilinear approach

In this paper, we explore the characteristics of lump and interaction solutions for a (1+1) dimensional Boussinesq equation. By employing the Hirota bilinear method, we derive and analyze the exact solutions of this equation. Specifically, we achieve the lump with bright-bright soliton solution, 1-lump,2-lumps and 3-lumps with single bright soliton solution, lump with periodic, kink, and anti-kink soliton solutions. Alongside deriving these solutions, we also illustrate their dynamic properties through graphical simulations. The Boussinesq equation holds significant importance due to its applications in various domains, such as water wave modeling, coastal engineering, and the numerical simulation of water wave dynamics in harbors and shallow seas. Our research shows that the employed method is straightforward, easy to understand, and highly efficient, providing valuable insights into the equation’s nature and its practical applications.

Alkyl polyglycosides derived from α-olefins via Fisher glycosidation and their adsorption and aggregation behavior in aqueous solution

The effective and stable use of α-olefins is a topic of great research interest due to their abundant reserves, and the fact that the hydrolysis and epoxidation reaction of these substances produces hydroxyl group as a key linking group plays an important role in the synthesis of surfactants. Consequently, a series of alkyl polyglycosides (DC08PG, DC10PG, and DC12PG) were synthesized as non-ionic surfactants via the glycosidation reaction of long-chain 1, 2-vicinal diol with different carbon numbers and glucose. The results showed that 1, 2-vicinal diol exhibited increased reactivity in glycosidation due to their unique molecular structure. Furthermore, it was observed that the degree of polymerization (DP) achieved was notably elevated, registering at 1.63, surpassing the DP of 1.37 typically prepared using conventional methods. This enhancement was paralleled by a demonstrable increase in hydrophilicity, as evidenced by the hydrophile-lipophile balance number (HLB), resulting in a substantial improvement in the water solubility of the product, the transmission rate > 90 %. For adsorption and aggregation behavior, DC12PG showed a smaller cross-sectional area (Amin), larger saturation adsorption (Γmax), and could aggregate to form micelles at low concentrations, and short-term dynamic adsorption properties (DST) was prominent. At the same concentration, for foam properties, DC12PG with longer alkyl chains produced higher and more stable foam; for emulsification properties, the emulsification time was 298 s; for wetting properties, the contact angle was 61.59° in 30 s. This analysis will help to reveal the intrinsic connection between the molecular structure and properties of surfactants.

Understanding the pressure effect on the physical properties of half-Heusler semiconductor LiCaX (X = As, Sb, N) compounds from Ab-initio calculations

The study delves into the structural, elastic, electronic, thermodynamic, and lattice dynamical and optic properties of LiCaX (X = As, Sb, N) ternary half-Heusler compounds under varying pressure and temperature conditions. Employing density functional theory with the generalized gradient approximation (GGA) in VASP codes, the initial steps involve optimizing the structure of the compound (cubic MgAgAs-type, space group F43m, C1b), determining elastic constants (C11, C12, and C44), and calculating elastic moduli (bulk modulus, shear modulus, Young's modulus). Other mechanical parameters such as Pugh's ratio, Poisson's ratio, and Zener anisotropy factor are also derived, providing insights into the brittle/ductile characteristics and isotropic/anisotropic behavior. The study further explores different vibrational modes in the compounds, and the effects of pressure on elastic anisotropy, vibrational, and optical properties are thoroughly investigated. Utilizing the quasi-harmonic Debye model, the research successfully reports V/Vo, bulk modulus, thermal expansion coefficient, and heat capacity at constant volume over a temperature range from 0 to 1000 K. The variation of photon energy is analyzed concerning the real and imaginary parts of the dielectric constant, refractive indices, extinction coefficient, reflectivity, and energy loss function up to 20 eV. The findings encapsulate the fundamental physical properties of all considered compounds, concluding with suggestions for potential future research avenues.

Structural Fluctuation in Homodimeric Aminoacyl-tRNA Synthetases Induces Half-of-the-Sites Activity.

Enzymatic activity is regulated by various mechanisms to ensure biologically proper functions. Notable instances of such regulation in homodimeric enzymes include "all-of-the-sites activity" and "half-of-the-sites activity". The difference in these activities lies in whether one or both of the subunits are simultaneously active. Owing to its uniqueness, the mechanism of half-of-the-sites activity has been widely investigated. Consequently, structural asymmetry derived from cooperative motion is considered to induce half-of-the-sites activity. In contrast, recent investigations have suggested that subunit-intrinsic properties or structural fluctuation also induces structural asymmetry. Hence, the mechanism underlying half-of-the-sites activity has not been completely elucidated. Additionally, most previous studies have focused only on half-of-the-sites activity. Therefore, by comparing the structural and dynamical properties of two representative homodimers exhibiting all-of-the-sites and half-of-the-sites activities, respectively, we attempted to elucidate the mechanism of half-of-the-sites activity. Specifically, all-atom molecular dynamics simulations were applied to lysyl-tRNA synthetase and tyrosyl-tRNA synthetase. Our analysis revealed that structural fluctuation is sufficient to induce structural asymmetry in addition to the well-established factor of cooperative motion. Considering that structural fluctuation is a common characteristic of any enzyme, it could be a general factor in half-of-the-sites activity.

Effect of layering and pre-loading on the dynamic properties of sand-rubber specimens in resonant column tests

AbstractSeveral studies show that scrap tyre rubber mixed with sand is an effective and sustainable method for mitigating vibrations. The dynamic and cyclic response of this composite soil has already been investigated. However, layered sand-rubber configurations have not been considered yet. This study reports findings of resonant column tests on three types of specimen: (a) sand-only or rubber-only, (b) layered sand-rubber, and (c) sand-rubber mixtures. The analysis allowed for an evaluation of the maximum shear modulus and its degradation with strain over a wide range of confining stress and shear strain. The evolution of the damping ratio with strain was determined analogously. Effects of pre-loading and pre-straining were also considered. The results show that the behaviour of layered specimens is much more similar to that of pure rubber than to sand-rubber mixtures, with very low shear modulus values, smaller degradation of stiffness with strain and pre-loading, and higher damping. For example, at the confining stress of 100 kPa and rubber content of 0/33.3/50/67.7/100% by volume, the small strain shear moduli for sand-rubber mixtures are equal to 98.3/30.4/15.4/7.1/1.3 MPa and 98.3/3.6-4.2/2.4-2.8/2.1/1.3 MPa for sand-rubber layered specimens, depending on the arrangement of layers. A shear beam model is shown to be adequate for calculating the response of the layered specimens comprising layers of large stiffness contrast.

Dynamic magnetic properties and magnetocaloric effect of a nanotube encapsulated with X36

Abstract Using Monte Carlo simulation, the dynamic magnetic properties and magnetocaloric effect of a mixed-spin (3/2, 2) single-walled nanotube encapsulated with X36 was studied, where X denotes the magnetic atom. The effects of intrinsic parameters on dynamic order parameters, magnetic susceptibility, internal energy, and specific heat were considered. The phase diagrams were obtained. The results indicate that the critical temperature can be increased by decreasing the absolute values of the anisotropies (Da, Db), increasing the exchange couplings (|Jab|, Jbb), and decreasing the amplitude h0 and the period τ of the external magnetic field. And under the influence of these parameters, the magnetocaloric effect is generated.

Indicators for Assessing the Combustion Intensity of Coal Particles Using a Single UV Sensor

This paper deals with the evaluation of the combustion intensity of coal particles on the basis of measurement data (UV radiation) from a scanning point photodiode. UV radiation is measured using a custom UV scanner at different distances from the burner in the vertical combustion chamber. The designed scanner uses a sensitive silicon carbide (SiC) photodiode, and its dynamical properties are investigated in the present work. Subsequently, experiments are performed for coal particles at different combustion temperatures and at different measuring locations of the scanner. The measurement data are processed in the frequency domain using the proposed algorithm, and two indicators for evaluating the combustion intensity are proposed. The obtained results show that the proposed indicators provide unequivocal information about the combustion intensity as a function of the combustion temperature.

Effect of Proteins on the Vulcanized Natural Rubber Crosslinking Network Structure and Mechanical Properties

Proteins are important factors affecting the properties of natural rubber. Therefore, investigating the effect of free and bonded proteins on the structure and mechanical properties of the vulcanized crosslinking network of natural rubber would provide a theoretical basis for the production of high mechanical resistance natural rubber. Herein, natural rubbers with different protein contents and types were prepared by high-speed centrifugation. And, the effects on their network structure, vulcanization, tensile strength, tearing strength and dynamic mechanical properties were investigated. The results showed that the reduction in protein content led to the decrement in the entanglement networks, crosslinking density and tensile and tear strengths of the vulcanized natural rubber. Moreover, the bonded proteins had an obvious influence on the vulcanization process, while free proteins played an important role in the crosslink densities. These results reveal that both bonded and free proteins are involved in the vulcanization process and the construction of the vulcanized crosslinking network structure of natural rubber, which enhances the mechanical properties such as the modulus and tensile strength of vulcanized natural rubber.

Electronic structure, phonons, and born effective charges in CuLaO2: A first-principles study

This study presents a first-principles investigation of the structural, electronic, dielectric, and dynamical properties of CuLaO2 in its rhombohedral delafossite phase using density functional theory. Our analysis reveals that CuLaO2 is a stable indirect band gap semiconductor with a 2.35 eV band gap, showing significant Cu (3d, 4s) and O (2p) orbital hybridization. Phonon dispersion calculations confirm dynamical stability with no imaginary frequencies, and the material exhibits anisotropic dielectric behavior due to mixed ionic-covalent bonding. These findings suggest that CuLaO2 has potential applications in optoelectronics and energy technologies, providing a theoretical basis for future experimental validation.