Folding Speed Research Articles

Comparison of Vocal Amplitude and Contact Speed according to SOVTE Type

Objectives: Observation of vocal fold vibration during semi-occluded vocal tract exercises (SOVTE) can help in understanding voice production due to semi-occlusion. This study aimed to investigate the differences in vocal fold vibration characteristics among various types of SOVTE. This study may provide valuable evidence to support more specific and effective methods in applying SOVTE to voice therapy. Methods: A total of 10 healthy young adults (5 males, 5 females) with a mean age of 24.28±4.54 years participated in the study. None of the participants had any voice-related diseases or were smokers. The participants performed various types of SOVTE including humming, voiced bilabial fricative, straw phonation, and water-resistance straw phonation. The authors measured the amplitude and contact speed of vocal fold using a vibration simulator and digital kymography (DKG). Results: The results showed that vocal fold amplitude was not significantly different among types of SOVTE, but there were significant differences in vocal fold contact speed (<i>p</i>=.046). In multiple comparisons, vocal fold contact speed was significantly faster in humming (<i>p</i>=.031) and water-resistance straw phonation (<i>p</i>=.018) compared to straw phonation. Conclusion: The difference in vocal fold contact speed indicates that the vocal fold vibration during SOVTE is affected by the shape of the vocal tract. The use of humming and water-resistance straw phonation can be an effective approach to improve voice quality by increasing vocal fold contact speed, which is a key factor in determining overall voice quality. These two methods can be useful in voice therapy after laryngeal microsurgery. In the field, conducting trial therapy rather than applying voice therapy according to the hierarchy of SOVTE may lead to successful results. SD children articulate phoneme sequences more segmentally in unlearned nonword contexts.

Effects of altered backbone composition on the folding kinetics and mechanism of an ultrafast-folding protein.

Sequence-encoded protein folding is a ubiquitous biological process that has been successfully engineered in a range of oligomeric molecules with artificial backbone chemical connectivity. A remarkable aspect of protein folding is the contrast between the rapid rates at which most sequences in nature fold and the vast number of conformational states possible in an unfolded chain with hundreds of rotatable bonds. Research efforts spanning several decades have sought to elucidate the fundamental chemical principles that dictate the speed and mechanism of natural protein folding. In contrast, little is known about how protein mimetic entities transition between an unfolded and folded state. Here, we report effects of altered backbone connectivity on the folding kinetics and mechanism of the B domain of Staphylococcal protein A (BdpA), an ultrafast-folding sequence. A combination of experimental biophysical analysis and atomistic molecular dynamics simulations performed on the prototype protein and several heterogeneous-backbone variants reveal the interplay among backbone flexibility, folding rates, and structural details of the transition state ensemble. Collectively, these findings suggest a significant degree of plasticity in the mechanisms that can give rise to ultrafast folding in the BdpA sequence and provide atomic level insights into how protein mimetic chains adopt an ordered folded state.

Design and Characteristics of Shape Memory Alloy Bidirectional Torsional Actuator

To overcome the problems of the low power/weight ratio of traditional servo motors, complex transmission systems, and large space occupied by hydraulic drive systems, this paper designs a bidirectional torsional actuator using the shape memory effect of Ti-Ni shape memory alloy (SMA) wire, which aims to realize the folding and unfolding of the wings of flying cars. The model of the designed actuator was established and the theoretical calculation was analyzed, based on which the experimental verification was carried out. It is found that when the heating current is 1.6 A, the mechanism can take into account the economy under the premise of meeting a certain folding speed. When the pre-stretching amount of SMA wire is 3%, the residual strain corresponding to the wire is small, about 0.577%, and it can provide driving torque and torsion angle to meet the design requirements of the actuator. This verifies the feasibility of the actuator and obtains the driving characteristics of the actuator. Finally, the shortcomings and improvement measures of the actuator are analyzed briefly.

Aerodynamic Characteristics of a Z-Shaped Folding Wing

Z-shaped folding wings have the potential to enhance the flight performance of an aircraft, contingent upon its mission requirements. However, the current scope of research on unmanned aerial vehicles (UAVs) with Z-shaped folding wings primarily focuses on the analysis of their folding structure and aeroelasticity-related vibrations. Computational fluid dynamics methods and dynamic meshing are employed to examine the folding process of Z-shaped folding wings. By comparing the steady aerodynamic characteristics of Z-shaped folding wings with those of conventional wings, this investigation explores the dynamic aerodynamic properties of Z-shaped folding wings at varying upward folding speeds. The numerical findings reveal that the folding of Z-shaped folding wings reduces the lift-to-drag ratio, yet simultaneously diminishes the nose-down pitching moment, thereby augmenting maneuverability. Concerning unsteady aerodynamics, the transient lift and drag coefficients of the folded wing initially increase and subsequently decrease as the folding angle increases at small angles of attack. Likewise, the nose-down pitching moment exhibits the same pattern in response to the folding angle. Additionally, the aerodynamic coefficients experience a slight decrease during the initial half of the folding process with increasing folding speed. Once the wing reaches approximately 40°~45° of folding, there is an abrupt change in the transient aerodynamic coefficients. Notably, this abrupt change is delayed with higher folding speeds, eventually converging to similar values across different folding speeds.

Robust membrane protein tweezers reveal the folding speed limit of helical membrane proteins.

Single-molecule tweezers, such as magnetic tweezers, are powerful tools for probing nm-scale structural changes in single membrane proteins under force. However, the weak molecular tethers used for the membrane protein studies have limited the observation of long-time, repetitive molecular transitions due to force-induced bond breakage. The prolonged observation of numerous transitions is critical in reliable characterizations of structural states, kinetics, and energy barrier properties. Here, we present a robust single-molecule tweezer method that uses dibenzocyclooctyne cycloaddition and traptavidin binding, enabling the estimation of the folding 'speed limit' of helical membrane proteins. This method is >100 times more stable than a conventional linkage system regarding the lifetime, allowing for the survival for ~12 hr at 50 pN and ~1000 pulling cycle experiments. By using this method, we were able to observe numerous structural transitions of a designer single-chained transmembrane homodimer for 9 hr at 12 pN and reveal its folding pathway including the hidden dynamics of helix-coil transitions. We characterized the energy barrier heights and folding times for the transitions using a model-independent deconvolution method and the hidden Markov modeling analysis, respectively. The Kramers rate framework yields a considerably low-speed limit of 21 ms for a helical hairpin formation in lipid bilayers, compared to μs scale for soluble protein folding. This large discrepancy is likely due to the highly viscous nature of lipid membranes, retarding the helix-helix interactions. Our results offer a more valid guideline for relating the kinetics and free energies of membrane protein folding.

RNA Folding Based on 5 Beads Model and Multiscale Simulation.

RNA folding prediction is very meaningful and challenging. The molecular dynamics simulation (MDS) of all atoms (AA) is limited to the folding of small RNA molecules. At present, most of the practical models are coarse grained (CG) model, and the coarse-grained force field (CGFF) parameters usually depend on known RNA structures. However, the limitation of the CGFF is obvious that it is difficult to study the modified RNA. Based on the 3 beads model (AIMS_RNA_B3), we proposed the AIMS_RNA_B5 model with three beads representing a base and two beads representing the main chain (sugar group and phosphate group). We first run the all atom molecular dynamic simulation (AAMDS), and fit the CGFF parameter with the AA trajectory. Then perform the coarse-grained molecular dynamic simulation (CGMDS). AAMDS is the foundation of CGMDS. CGMDS is mainly to carry out the conformation sampling based on the current AAMDS state and improve the folding speed. We simulated the folding of three RNAs, which belong to hairpin, pseudoknot and tRNA respectively. Compared to the AIMS_RNA_B3 model, the AIMS_RNA_B5 model is more reasonable and performs better.

The Influence of the Selection at the Amino Acid Level on Synonymous Codon Usage from the Viewpoint of Alternative Genetic Codes

Synonymous codon usage can be influenced by mutations and/or selection, e.g., for speed of protein translation and correct folding. However, this codon bias can also be affected by a general selection at the amino acid level due to differences in the acceptance of the loss and generation of these codons. To assess the importance of this effect, we constructed a mutation-selection model model, in which we generated almost 90,000 stationary nucleotide distributions produced by mutational processes and applied a selection based on differences in physicochemical properties of amino acids. Under these conditions, we calculated the usage of fourfold degenerated (4FD) codons and compared it with the usage characteristic of the pure mutations. We considered both the standard genetic code (SGC) and alternative genetic codes (AGCs). The analyses showed that a majority of AGCs produced a greater 4FD codon bias than the SGC. The mutations producing more thymine or adenine than guanine and cytosine increased the differences in usage. On the other hand, the mutational pressures generating a lot of cytosine or guanine with a low content of adenine and thymine decreased this bias because the nucleotide content of most 4FD codons stayed in the compositional equilibrium with these pressures. The comparison of the theoretical results with those for real protein coding sequences showed that the influence of selection at the amino acid level on the synonymous codon usage cannot be neglected. The analyses indicate that the effect of amino acid selection cannot be disregarded and that it can interfere with other selection factors influencing codon usage, especially in AT-rich genomes, in which AGCs are usually used.

Fast Bayesian inference for inverse heat conduction problem using polynomial chaos and Karhunen–Loeve expansions

We present a fast Bayesian inference framework for solving inverse heat conduction problems (IHCP) for the estimation of boundary heat flux. The framework leverages the polynomial chaos expansions (PCEs) for generating computationally efficient and statistically equivalent surrogate model of the computationally expensive forward model and dimensionality reduction based on Karhunen–Loeve (K–L) expansion. We demonstrate the potential of this approach using three model problems to estimate heat flux in inverse heat conduction models. We represent the heat flux using K–L expansion to reduce the high dimensionality of the heat flux and compute the posterior probability distribution of the heat flux using the temperature measurements. The first inverse problem involves the estimation of time–varying heat flux in a one–dimensional slab using transient temperature measurements. The second problem involves the estimation of the unknown time–dependent heat flux of the disc in a realistic axisymmetric disc brake system. The third problem involves the estimation of the surface heat flux on a sounding rocket having a realistic three–dimensional geometry of the rocket module used in actual flight tests. We further obtain the inverse solution by computing the expectation of the distribution and demonstrate that this approach becomes orders of magnitude more efficient when we use the PCE surrogate model instead of the direct forward model for comparable accuracy. The numerical results show that this framework overcomes the drawback of high computational cost of Markov chain Monte Carlo (MCMC) without compromising on solution accuracy. The combination of PC–based surrogate modeling and K–L based dimensionality reduction leads to over 2000–fold speed up of numerical solution of IHCP.

A space deployable antenna model based on shape memory alloy composite with folding‐deploying two‐way behavior

AbstractIn this study, a flexible space deployable antenna model with good self‐folding and deploying two‐way shape memory effect is proposed and prepared based on shape memory alloy composite strips and polyimide thin film. The thickness and cyclic properties of the shape memory alloy strip were considered for the two‐way shape memory effect. Good self‐folding at 110°C and self‐deploying at 20°C for 10 min were demonstrated. Moreover, the Joule heating method was applied to improve the folding speed within 90 s. The two‐way shape memory effect with reversible self‐folding and deploying behavior of the space deployable antennas is aimed at improving avoidance of space debris in future applications.

Microphase Separation‐Driven Sequential Self‐Folding of Nanocomposite Hydrogel/Elastomer Actuators

AbstractUntethered stimuli‐responsive soft materials with programmed sequential self‐folding are of great interest due to their ability to achieve task‐specific shape transformation with complex final configuration. Here, reversible and sequential self‐folding soft actuators are demonstrated by utilizing a temperature‐responsive nanocomposite hydrogel with different folding speeds but the same chemical composition. By varying the UV light intensity during the photo‐crosslinking of the nanocomposite hydrogel, different types of microstructures can be realized via phase separation mechanisms, which allow to control the folding speeds. The self‐folding structures are fabricated by integrating two dissimilar materials (i.e., a nanocomposite hydrogel and an elastomer) into hinge‐based bilayer structures via extrusion‐based 3D printing. It has been demonstrated that the folding kinetics can be accelerated by more than one order of magnitude due to the phase‐separated microstructure formed by the relatively weaker UV intensity (≈10 mW cm‐2) compared to the one formed by stronger UV intensity (≈100 mW cm‐2). 3D structures with sequential self‐folding capabilities are realized by prescribing actuation speeds and folding angles to specific hinges of the nanocomposite hydrogel. Sequential folding box and self‐locking latch structures are fabricated to demonstrate the ability to capture and hold objects underwater.

Effect of U-Flex-to-Install and Dynamic U-Flexing on Li-Ion Battery State of Health Degradation Subjected to Varying Fold Orientations, Folding Speeds, Depths of Charge, C-Rates, and Temperatures

Abstract The demand for wearable consumer electronics, fitness accessories, and biomedical equipment has led to the growth research and development of thin flexible batteries. Wearable equipment and other asset monitoring applications require conformal installation of power sources on nonplanar surfaces. For power sources in wearable electronics, durability to sustain repetitive mechanical stresses induced by human body motion is paramount along with the usual desirable power source characteristics. Previous research documenting the reliability of statically and dynamically folded power sources is scarce and does not follow standardized test protocols. Particularly, the use of manual stressing for mechanical folding of the power sources instead of a mechanical test setup is a key shortcoming in existing literature. Data are lacking on battery life cycling and in situ mechanical stress-testing of the power sources including their impact of performance and reliability. This study aims to overcome these deficiencies by testing a commercial Li-ion power source under static as well as dynamic folding. Furthermore, the fold orientation and its fold speed are varied to evaluate the effect of different mechanical stress topologies on the power source. Finally, a regression model was developed to capture the effect of these use parameters on battery capacity degradation.

Increased expression of the fluorescent reporter protein ymNeonGreen in Saccharomyces cerevisiae by reducing RNA secondary structure near the start codon.

Expression of a new fluorescent reporter protein called mNeonGreen, that is not based on the jellyfish green fluorescent protein (GFP) sequence, shows increased brightness and folding speed compared to enhanced GFP. However, in vivo brightness of mNeonGreen and its yeast-optimized variant ymNeonGreen in S. cerevisiae is lower than expected, limiting the use of this high quantum yield, fast-folding reporter in budding yeast. This study shows that secondary RNA structure near the start codon in the ymNeonGreen ORF inhibits expression in S. cerevisiae. Removing secondary structure, without altering the ymNeonGreen protein sequence, led to a 2 and 4-fold increase in fluorescence when expressed in S. cerevisiae and E. coli, respectively. In S. cerevisiae, increased fluorescence was seen with strong and weak promoters and led to higher transcript levels suggesting greater transcript stability and improved expression in the absence of stable secondary RNA structure near the start codon.

A steering control system for the tractor – semi-trailer combination vehicle with the electromechanical transmission

The article offers an algorithm for the operation of the steering and active drive control system of a saddle-type tractor – trailer combination. The algorithm allows reducing the width of the cornering corridor when maneuvering at low speeds. In the combination vehicle under study, all the wheels of the tractor and semi-trailer are driving and steered. The algorithm of the steering control system takes into account the current values of the folding angle and speed of the combination vehicle. The active drive control is based on the analysis of the forces in the coupling device. The efficiency and effectiveness of the proposed algorithm has been proved using computational experiments.

Single laser trapping for optical folding and rotation of red blood cells in sickle cell disease in response to hydroxyurea treatment

Optical folding and rotation behavior of red blood cells (RBCs) in polarized laser tweezers are considerably important for understanding the biophysical and biomechanical properties using the fast probing method. Here, a dual-mode polarized single-laser tweezers technique with distinct principal axes exhibiting different polarization states is presented and designed to investigate the deformation, optical folding, and rotation of single living cells with one measurement. RBC optical folding and rotation speed are measured in patients with sickle cell disease (SCD), including follow up of patients after hydroxyurea (HU) treatment for at least three months. Folding angle and rotation speed are significantly lower in patients with SCD and do not significantly differ in patients treated by HU compared with the healthy control group. The RBC folding angle and rotation speed in patients treated with HU drug increase linearly at lower laser powers and rapidly at higher powers, and increase much slowly in patients not treated with HU. The difference in the folding angle and rotation speed of RBCs could be useful for drug response in SCD or predicting pain crisis in SCD.

Box Folding Machine Design by Using Product Design Method Functional Based Model

In order to meet the growing demand for products, scientists have been developing product design methods. Based on the existing product design methods and the Oregon State University’s Modern Product Design, this report talks about the improved product design method and uses this method to design one new cases. The example case is box folding machine. It consists of a feeding system, a transport system, a folding system, and an exporting system. The core part folding system consists of a two-step folding system. By folding twice, the finished box is wrapped and self-locking. Through the final estimation, the folding speed of the box folding assembly line is five times that of manual folding. As a result, the box folding assembly line can meet the needs of fast folding.

Exploring the Evolutionary History of Kinetic Stability in the α-Lytic Protease Family.

In addition to encoding the tertiary fold and stability, the primary sequence of a protein encodes the folding trajectory and kinetic barriers that determine the speed of folding. How these kinetic barriers are encoded is not well understood. Here, we use evolutionary sequence variation in the α-lytic protease (αLP) protein family to probe the relationship between sequence and energy landscape. αLP has an unusual energy landscape: the native state of αLP is not the most thermodynamically favored conformation and, instead, remains folded due to a large kinetic barrier preventing unfolding. To fold, αLP utilizes an N-terminal pro region similar in size to the protease itself that functions as a folding catalyst. Once folded, the pro region is removed, and the native state does not unfold on a biologically relevant time scale. Without the pro region, αLP folds on the order of millennia. A phylogenetic search uncovers αLP homologs with a wide range of pro region sizes, including some with no pro region at all. In the resulting phylogenetic tree, these homologs cluster by pro region size. By studying homologs naturally lacking a pro region, we demonstrate they can be thermodynamically stable, fold much faster than αLP, yet retain the same fold as αLP. Key amino acids thought to contribute to αLP's extreme kinetic stability are lost in these homologs, supporting their role in kinetic stability. This study highlights how the entire energy landscape plays an important role in determining the evolutionary pressures on the protein sequence.

A RECONFIGURABLE DATA FLOW ARCHITECTURE FOR SIGNAL PROCESSING APPLICATIONS

This paper aims to devise a data flow model of computation for signal processing applications in which the operational nodes are signal/image processing functions such as Pixsum, Edge, Smooth. These functions are configured during run time from a pool of reconfigurable FPGAS. Thus because of the data flow model of computation, the signal processing functions execute concurrently. At the same time, these functions by exploiting their inherent spatial parallelism execute at high speed. There is a two fold speed up in the execution of image/signal processing applications one at the architecture level wherein a node of the dataflow model executes a digital signal processing (DSP) function rather than a low level machine operation. The second speed up is due to the fact that each DSP function is configured to execute in an FPGA by using maximally the concurrent operations that such a function permits. Another significant benefit that arises from our proposed architecture is that by reconfiguring an FPGA for a DSP function at run time, the reusability of the hardware elements results in reduced cost of operations. In this paper we provide an outline of the data flow architecture and its operational aspects.

Mechanical characteristics of orally disintegrating films: Comparison of folding endurance and tensile properties.

The tensile test is the most widely used method for testing the mechanical characteristics of orally disintegrating films (ODFs). The other available test is the folding endurance (FE) test, which is more suitable for clarifying the actual strength during the manufacturing and dosing. However, the FE test is performed manually, and the FE number it generates has not been adequately analyzed as an index. The aim of this studies were to establish an automatic method for determining the FE number, and to compare the resulting FE numbers with the tensile properties. For this purpose, a desktop-model endurance test machine was used. First, the operating conditions-i.e., the folding angle, the folding speed and the weight requirement were optimized using ODF models. Secondly, the FE of ODFs prepared from three film formers (HPMC, HPC, and PVA) and with insoluble particles (calcium carbonate), plasticizers (glycerin) and APIs (acetaminophen), was evaluated and compared with the tensile properties. Lastly, the commercial ODFs were investigated. The results showed that our automatic system could be successfully used to determine the FE characteristics of ODFs. FE was suggested to relate to not only the strength but also the elongation during the tensile test.

Effect of Protein Structure on Evolution of Cotranslational Folding

Cotranslational folding depends on the folding speed and stability of the nascent protein. It remains difficult, however, to predict which proteins cotranslationally fold. Here, we simulate evolution of model proteins to investigate how native structure influences evolution of cotranslational folding. We developed a model that connects protein folding during and after translation to cellular fitness. Model proteins evolved improved folding speed and stability, with proteins adopting one of two strategies for folding quickly. Low contact order proteins evolve to fold cotranslationally. Such proteins adopt native conformations early on during the translation process, with each subsequently translated residue establishing additional native contacts. On the other hand, high contact order proteins tend not to be stable in their native conformations until the full chain is nearly extruded. We also simulated evolution of slowly translating codons, finding that slower translation speeds at certain positions enhances cotranslational folding. Finally, we investigated real protein structures using a previously published data set that identified evolutionarily conserved rare codons in Escherichia coli genes and associated such codons with cotranslational folding intermediates. We found that protein substructures preceding conserved rare codons tend to have lower contact orders, in line with our finding that lower contact order proteins are more likely to fold cotranslationally. Our work shows how evolutionary selection pressure can cause proteins with local contact topologies to evolve cotranslational folding.

Elastically and Plastically Foldable Electrothermal Micro‐Origami for Controllable and Rapid Shape Morphing

AbstractIntegrating origami principles within traditional microfabrication methods can produce shape morphing microscale metamaterials and 3D systems with complex geometries and programmable mechanical properties. However, available micro‐origami systems usually have slow folding speeds, provide few active degrees of freedom, rely on environmental stimuli for actuation, and allow for either elastic or plastic folding but not both. This work introduces an integrated fabrication–design–actuation methodology of an electrothermal micro‐origami system that addresses the above‐mentioned challenges. Controllable and localized Joule heating from electrothermal actuator arrays enables rapid, large‐angle, and reversible elastic folding, while overheating can achieve plastic folding to reprogram the static 3D geometry. Because the proposed micro‐origami do not rely on an environmental stimulus for actuation, they can function in different atmospheric environments and perform controllable multi‐degrees‐of‐freedom shape morphing, allowing them to achieve complex motions and advanced functions. Combining the elastic and plastic folding enables these micro‐origami to first fold plastically into a desired geometry and then fold elastically to perform a function or for enhanced shape morphing. The proposed origami systems are suitable for creating medical devices, metamaterials, and microrobots, where rapid folding and enhanced control are desired.