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Journal articles on the topic 'Backbone dynamic'

Author: Grafiati

Published: 11 March 2023

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1

Kharchenko, Vladlena, Michal Nowakowski, Mariusz Jaremko, Andrzej Ejchart, and Łukasz Jaremko. "Dynamic 15N{1H} NOE measurements: a tool for studying protein dynamics." Journal of Biomolecular NMR 74, no. 12 (September 12, 2020): 707–16. http://dx.doi.org/10.1007/s10858-020-00346-6.

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AbstractIntramolecular motions in proteins are one of the important factors that determine their biological activity and interactions with molecules of biological importance. Magnetic relaxation of 15N amide nuclei allows one to monitor motions of protein backbone over a wide range of time scales. 15N{1H} nuclear Overhauser effect is essential for the identification of fast backbone motions in proteins. Therefore, exact measurements of NOE values and their accuracies are critical for determining the picosecond time scale of protein backbone. Measurement of dynamic NOE allows for the determination of NOE values and their probable errors defined by any sound criterion of nonlinear regression methods. The dynamic NOE measurements can be readily applied for non-deuterated or deuterated proteins in both HSQC and TROSY-type experiments. Comparison of the dynamic NOE method with commonly implied steady-state NOE is presented in measurements performed at three magnetic field strengths. It is also shown that improperly set NOE measurement cannot be restored with correction factors reported in the literature.

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2

YE, JIEPING, RAVI JANARDAN, and SONGTAO LIU. "PAIRWISE PROTEIN STRUCTURE ALIGNMENT BASED ON AN ORIENTATION-INDEPENDENT BACKBONE REPRESENTATION." Journal of Bioinformatics and Computational Biology 02, no. 04 (December 2004): 699–717. http://dx.doi.org/10.1142/s021972000400082x.

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Determining structural similarities between proteins is an important problem since it can help identify functional and evolutionary relationships. In this paper, an algorithm is proposed to align two protein structures. Given the protein backbones, the algorithm finds a rigid motion of one backbone onto the other such that large substructures are matched. The algorithm uses a representation of the backbones that is independent of their relative orientations in space and applies dynamic programming to this representation to compute an initial alignment, which is then refined iteratively. Experiments indicate that the algorithm is competitive with two well-known algorithms, namely DALI and LOCK.

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3

Walker, Ian D. "Continuous Backbone “Continuum” Robot Manipulators." ISRN Robotics 2013 (July 16, 2013): 1–19. http://dx.doi.org/10.5402/2013/726506.

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This paper describes and discusses the history and state of the art of continuous backbone robot manipulators. Also known as continuum manipulators, these robots, which resemble biological trunks and tentacles, offer capabilities beyond the scope of traditional rigid-link manipulators. They are able to adapt their shape to navigate through complex environments and grasp a wide variety of payloads using their compliant backbones. In this paper, we review the current state of knowledge in the field, focusing particularly on kinematic and dynamic models for continuum robots. We discuss the relationships of these robots and their models to their counterparts in conventional rigid-link robots. Ongoing research and future developments in the field are discussed.

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Dent, Erik W., Elliott B. Merriam, and Xindao Hu. "The dynamic cytoskeleton: backbone of dendritic spine plasticity." Current Opinion in Neurobiology 21, no. 1 (February 2011): 175–81. http://dx.doi.org/10.1016/j.conb.2010.08.013.

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5

Bertini, Ivano, Donald A. Bryant, Stefano Ciurli, Alexander Dikiy, Claudio O. Fernández, Claudio Luchinat, Niyaz Safarov, Alejandro J. Vila, and Jindong Zhao. "Backbone Dynamics of Plastocyanin in Both Oxidation States." Journal of Biological Chemistry 276, no. 50 (August 16, 2001): 47217–26. http://dx.doi.org/10.1074/jbc.m100304200.

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A model-free analysis based on15NR1,15NR2, and15N-1H nuclear Overhauser effects was performed on reduced (diamagnetic) and oxidized (paramagnetic) forms of plastocyanin fromSynechocystissp. PCC6803. The protein backbone is rigid, displaying a small degree of mobility in the sub-nanosecond time scale. The loops surrounding the copper ion, involved in physiological electron transfer, feature a higher extent of flexibility in the longer time scale in both redox states, as measured from D2O exchange of amide protons and from NH-H2O saturation transfer experiments. In contrast to the situation for other electron transfer proteins, no significant difference in the dynamic properties is found between the two redox forms. A solution structure was also determined for the reduced plastocyanin and compared with the solution structure of the oxidized form in order to assess possible structural changes related to the copper ion redox state. Within the attained resolution, the structure of the reduced plastocyanin is indistinguishable from that of the oxidized form, even though small chemical shift differences are observed. The present characterization provides information on both the structural and dynamic behavior of blue copper proteins in solution that is useful to understand further the role(s) of protein dynamics in electron transfer processes.

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Kim, Yeon Su, Kyeong Ho Moon, Se Ky Chang, and Jai Kyun Mok. "Strength Analysis of Chassis Structure for Medium-Sized Low-Floor Vehicle under Dynamic Load Cases." Key Engineering Materials 452-453 (November 2010): 709–12. http://dx.doi.org/10.4028/www.scientific.net/kem.452-453.709.

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For the medium-sized low-floor bus, backbone structure of chassis was designed to have light-weight structure with SAPH (Steel Automobile Press Hot rolled) 440. Strength for the designed backbone structure was also analyzed by finite element method under various dynamic load cases considered in this paper. On the basis of the analysis results, the structural safety for the designed backbone structure was evaluated and discussed in this paper.

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Saeedvand, Saeed, Hadi S. Aghdasi, and Leili Mohammad Khanli. "Novel Distributed Dynamic Backbone-based Flooding in Unstructured Networks." Peer-to-Peer Networking and Applications 13, no. 3 (November 18, 2019): 872–89. http://dx.doi.org/10.1007/s12083-019-00817-0.

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8

BONONI, LUCIANO, MARCO DI FELICE, and SARA PIZZI. "DBA-MAC: DYNAMIC BACKBONE-ASSISTED MEDIUM ACCESS CONTROL PROTOCOL FOR EFFICIENT BROADCAST IN VANETS." Journal of Interconnection Networks 10, no. 04 (December 2009): 321–44. http://dx.doi.org/10.1142/s0219265909002601.

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Active safety systems based on dissemination of alert messages are one of the most important applications of Vehicular ad Hoc Networks (VANETs). These systems typically require to provide efficient and reliable delivery of safety information to all the vehicles travelling over a geographical area. Reducing the delivery delay is also a crucial issue due to the real-time nature of the communication. To meet these requirements, in this paper we design a cross-layered MAC and clustering solution for the fast propagation of broadcast messages in a VANET. A distributed dynamic clustering algorithm is proposed in order to create a dynamic virtual backbone inside the vehicular network. The vehicle-members of the backbone are responsible for implementing an efficient message propagation. The backbone creation and maintenance are proactively performed aiming to balance the stability of backbone connections as well as cost/efficiency trade-off and hops-reduction when forwarding the broadcast messages. A fast multi-hop MAC forwarding scheme is defined to exploit the role of backbone vehicles, under a cross-layered approach. Simulation results show that our cross-layer scheme guarantees high message delivery ratio, reduces the delivery delay and provides efficient channel utilization when compared with other dissemination schemes for VANETs.

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9

Rong, Xiao Yang, Tian Hong Yang, Pei Tao Wang, Hong Wang, and Yang Li. "Dynamic Triaxial Test Research of Stage Change of Cohesive Soil." Applied Mechanics and Materials 353-356 (August 2013): 937–40. http://dx.doi.org/10.4028/www.scientific.net/amm.353-356.937.

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With the STX-50 pneumatic-typed dynamic triaxial system, the undrained dynamic triaxial tests on the saturated cohesive soil are performed to study the dynamic strength properties. The changing process of the dynamic strength, backbone curve and the soil deformation of the cohesive soil under dynamic load are zoom analysis by stages to get their regularity. It is found that the stage change of the dynamic strength, backbone curve and the soil deformation all exist, which the stage I of the soil deformation has little damage, the stage III is not allowed, the stage II is determined by the importance of the concrete and the sensitive degree to the deformation. In order to analysis the deformation stability and stress stability of the formation in the effect of the dynamic load, provide qualitative and quantitative basis for the soil dynamic study.

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10

Wu, Celimuge, Xianfu Chen, Yusheng Ji, Satoshi Ohzahata, and Toshihiko Kato. "Efficient Broadcasting in VANETs Using Dynamic Backbone and Network Coding." IEEE Transactions on Wireless Communications 14, no. 11 (November 2015): 6057–71. http://dx.doi.org/10.1109/twc.2015.2447812.

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11

Cuomo, Francesca, Izhak Rubin, Andrea Baiocchi, and Pierpaolo Salvo. "Enhanced VANET broadcast throughput capacity via a dynamic backbone architecture." Ad Hoc Networks 21 (October 2014): 42–59. http://dx.doi.org/10.1016/j.adhoc.2014.04.008.

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12

Mukherjee, Soma, William L. A. Brooks, Yuqiong Dai, and Brent S. Sumerlin. "Doubly-dynamic-covalent polymers composed of oxime and oxanorbornene links." Polymer Chemistry 7, no. 10 (2016): 1971–78. http://dx.doi.org/10.1039/c5py02046h.

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Two sets of reversible covalent linkages distributed in series along a polymer backbone were used to prepare a new class of doubly dynamic-covalent polymers capable of reversibly dissociatingviatwo distinct pathways.

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13

Lu, Weihong, Xiaowei An, Jian Zhu, Nianchen Zhou, Zhengbiao Zhang, Xiangqiang Pan, and Xiulin Zhu. "From seleno-mediated radical polymerization to seleno-containing branched polymers and dynamic hydrogel." RSC Advances 7, no. 16 (2017): 9773–79. http://dx.doi.org/10.1039/c6ra28565a.

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14

Qi, Xiaohan, and Zhihua Yang. "A Multi-MCDS scheduling based virtual backbone network construction and maintenance algorithm in FANET." MATEC Web of Conferences 189 (2018): 03013. http://dx.doi.org/10.1051/matecconf/201818903013.

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Constructing a virtual backbone network can efficiently concentrate most routing and forwarding operations of whole network into several dominating nodes in the virtual backbone sub-net, which is recently developing into an attracted candidate solution for the architectures of terrestrial mobile ad hoc networks. In a flying ad hoc network (FANET), however, high dynamics of nodes and scenarios produce considerably large challenges on the topology control and maintenance due to rapidly timevarying property of topology. In this paper, therefore, we proposed a link prediction-based minimal connected dominating set (MCDS) dependent topology control mechanism to achieve efficient maintenances of connectivity in the network. In particular, the proposed algorithm could provide a stable and effective virtual backbone sub-net in a fast changing topology of FANET, by flexibly scheduling multiple MCDS with a very efficient method. The simulation results shows that, compared with typical single CDS method, the proposed algorithm presents excellent performances in obviously dynamic environments with respect to fewer update times and higher rate of successful updates.

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15

Hong, Dongxiao, Thomas L. Hill, and Simon A. Neild. "Conditions for the existence of isolated backbone curves." Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 475, no. 2232 (December 2019): 20190374. http://dx.doi.org/10.1098/rspa.2019.0374.

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Isolated backbone curves represent significant dynamic responses of nonlinear systems; however, as they are disconnected from the primary responses, they are challenging to predict and compute. To explore the conditions for the existence of isolated backbone curves, a generalized two-mode system, which is representative of two extensively studied examples, is used. A symmetric two-mass oscillator is initially studied and, as has been previously observed, this exhibits a perfect bifurcation between its backbone curves. As this symmetry is broken, the bifurcation splits to form an isolated backbone curve. Here, it is demonstrated that this perfect bifurcation, indicative of a symmetric structure, may be preserved when the symmetry is broken under certain conditions; these are derived analytically. With the symmetry broken, the second example—a single-mode nonlinear structure with a nonlinear tuned mass damper—is considered. The evolution of the system's backbone curves is investigated in nonlinear parameter space. It is found that this space can be divided into several regions, within which the backbone curves share similar topological features, defining the conditions for the existence of isolated backbone curves. This allows these features to be more easily accounted for, or eliminated, when designing nonlinear systems.

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16

Park, Sangjoon, and Khalid M. Mosalam. "Simulation of Reinforced Concrete Frames with Nonductile Beam-Column Joints." Earthquake Spectra 29, no. 1 (February 2013): 233–57. http://dx.doi.org/10.1193/1.4000100.

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The accurate prediction of shear strength and flexibility of beam-column joints without transverse reinforcement is essential to assess the seismic performance of nonductile reinforced concrete (RC) buildings characterized by having such unreinforced beam-column joints. In this study, a multilinear backbone curve to represent the moment-rotation relationship of an unreinforced corner beam-column joint is proposed. The modeling parameters of the backbone curve are estimated based on experimental results of four corner joint specimens recently tested by the authors. Furthermore, the proposed backbone curve is modified to be applicable to interior and roof beam-column joints. These backbone curves are validated by accurate reproduction of the force-drift responses of the four corner joint specimens and eight other exterior and interior joint specimens from literature. Using these backbone curves, nonlinear dynamic analyses are performed on three hypothetical building frames. The analytical results demonstrate the importance of joint flexibility for seismic assessment of nonductile RC buildings.

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17

Tran, Nghiem Xuan, Bao Ngoc Nguyen, Byeong-Soo Yoo, and Sung-Ryul Kim. "Slope effect on dynamic p–y backbone curve in dry sand." Soil Dynamics and Earthquake Engineering 144 (May 2021): 106693. http://dx.doi.org/10.1016/j.soildyn.2021.106693.

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18

Yang, Zhao, and Qingshuang Sun. "A dynamic global backbone updating for communication-efficient personalised federated learning." Connection Science 34, no. 1 (August 25, 2022): 2240–64. http://dx.doi.org/10.1080/09540091.2022.2114428.

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19

Liang, B., and Z. J. Haas. "Hybrid routing in ad hoc networks with a dynamic virtual backbone." IEEE Transactions on Wireless Communications 5, no. 6 (June 2006): 1392–405. http://dx.doi.org/10.1109/twc.2006.1638660.

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20

Zhang, Haichang, Wei-Yao Tung, Xiang Li, Hailiang Jin, Ruonan Deng, Yu-Ming Chen, Yifan Mao, and Yu Zhu. "Conjugated polymer with dynamic and thermoreversible hydrogen bonding on the backbone." Polymer 203 (August 2020): 122787. http://dx.doi.org/10.1016/j.polymer.2020.122787.

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21

Herrera, Manuel, Marco Pérez-Hernández, Amit Kumar Jain, and Ajith Kumar Parlikad. "Critical link analysis of a national internet backbone via dynamic perturbation." IFAC-PapersOnLine 53, no. 3 (2020): 155–60. http://dx.doi.org/10.1016/j.ifacol.2020.11.025.

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22

Shin, Jeongkyu, George A. Mashour, Seungwoo Ku, Seunghwan Kim, and Uncheol Lee. "Subgraph “Backbone” Analysis of Dynamic Brain Networks during Consciousness and Anesthesia." PLoS ONE 8, no. 8 (August 15, 2013): e70899. http://dx.doi.org/10.1371/journal.pone.0070899.

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23

Valensin, Gianni, Elena Gaggelli, Andrea Lepri, and Alessandro Sega. "Motional and conformational dynamics in a homologous series of smooth muscle relaxing agents." Canadian Journal of Chemistry 64, no. 10 (October 1, 1986): 2048–52. http://dx.doi.org/10.1139/v86-338.

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Dynamic features were investigated in a homologous series of synthesized drugs having pharmacologic activity, with particular emphasis on relative motions of the two side chains anchored to a backbone of two aromatic rings linked by an amide bridge. A general and deep insight was reached by using a model-free approach. Conformational and motional dynamics within the compound exhibiting maximum activity were delineated and the most relevant parameters for pharmacologic action were defined.

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24

Rangadurai, Atul, Eric S. Szymanski, Isaac Kimsey, Honglue Shi, and Hashim M. Al-Hashimi. "Probing conformational transitions towards mutagenic Watson–Crick-like G·T mismatches using off-resonance sugar carbon R1ρ relaxation dispersion." Journal of Biomolecular NMR 74, no. 8-9 (August 12, 2020): 457–71. http://dx.doi.org/10.1007/s10858-020-00337-7.

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Abstract NMR off-resonance R1ρ relaxation dispersion measurements on base carbon and nitrogen nuclei have revealed that wobble G·T/U mismatches in DNA and RNA duplexes exist in dynamic equilibrium with short-lived, low-abundance, and mutagenic Watson–Crick-like conformations. As Watson–Crick-like G·T mismatches have base pairing geometries similar to Watson–Crick base pairs, we hypothesized that they would mimic Watson–Crick base pairs with respect to the sugar-backbone conformation as well. Using off-resonance R1ρ measurements targeting the sugar C3′ and C4′ nuclei, a structure survey, and molecular dynamics simulations, we show that wobble G·T mismatches adopt sugar-backbone conformations that deviate from the canonical Watson–Crick conformation and that transitions toward tautomeric and anionic Watson–Crick-like G·T mismatches restore the canonical Watson–Crick sugar-backbone. These measurements also reveal kinetic isotope effects for tautomerization in D2O versus H2O, which provide experimental evidence in support of a transition state involving proton transfer. The results provide additional evidence in support of mutagenic Watson–Crick-like G·T mismatches, help rule out alternative inverted wobble conformations in the case of anionic G·T−, and also establish sugar carbons as new non-exchangeable probes of this exchange process.

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25

Gao, Wenli, Rui Tang, Minghao Bai, Hengzhe Yu, Yonghong Ruan, Jinli Zheng, Yinjun Chen, and Wengui Weng. "Dynamic covalent polymer networks with mechanical and mechanoresponsive properties reinforced by strong hydrogen bonding." Polymer Chemistry 13, no. 15 (2022): 2173–77. http://dx.doi.org/10.1039/d2py00179a.

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Mechanoresponsive dynamic covalent networks were designed and synthesized by embedding radical mechanophores into the polymer backbone as crosslinkers. The mechanical properties and mechanoresponsiveness of the polymers were reinforced by hydrogen bonds.

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26

Wang, Hui, Yuan Li, Dong-mei Li, Bin Cui, and De-Sheng Liu. "Polaron spin filtering in an organic ferromagnetic polymer: a dynamics simulation." Physical Chemistry Chemical Physics 18, no. 1 (2016): 503–9. http://dx.doi.org/10.1039/c5cp05789b.

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27

Zhang, Mingzhen, Jie Zheng, Ruth Nussinov, and Buyong Ma. "Molecular Recognition between Aβ-Specific Single-Domain Antibody and Aβ Misfolded Aggregates." Antibodies 7, no. 3 (July 13, 2018): 25. http://dx.doi.org/10.3390/antib7030025.

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Aβ is the toxic amyloid polypeptide responsible for Alzheimer’s disease (AD). Prevention and elimination of the Aβ misfolded aggregates are the promising therapeutic strategies for the AD treatments. Gammabody, the Aβ-Specific Single-domain (VH) antibody, recognizes Aβ aggregates with high affinity and specificity and reduces their toxicities. Employing the molecular dynamics simulations, we studied diverse gammabody-Aβ recognition complexes to get insights into their structural and dynamic properties and gammabody-Aβ recognitions. Among many heterogeneous binding modes, we focused on two gammabody-Aβ recognition scenarios: recognition through Aβ β-sheet backbone and on sidechain surface. We found that the gammabody primarily uses the complementarity-determining region 3 (CDR3) loop with the grafted Aβ sequence to interact with the Aβ fibril, while CDR1/CDR2 loops have very little contact. The gammabody-Aβ complexes with backbone binding mode are more stable, explaining the gammabody’s specificity towards the C-terminal Aβ sequence.

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28

Hassan, Mohamed Khalafalla, Sharifah Hafizah Syed Ariffin, N. Effiyana Ghazali, Mutaz Hamad, Mosab Hamdan, Monia Hamdi, Habib Hamam, and Suleman Khan. "Dynamic Learning Framework for Smooth-Aided Machine-Learning-Based Backbone Traffic Forecasts." Sensors 22, no. 9 (May 9, 2022): 3592. http://dx.doi.org/10.3390/s22093592.

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Recently, there has been an increasing need for new applications and services such as big data, blockchains, vehicle-to-everything (V2X), the Internet of things, 5G, and beyond. Therefore, to maintain quality of service (QoS), accurate network resource planning and forecasting are essential steps for resource allocation. This study proposes a reliable hybrid dynamic bandwidth slice forecasting framework that combines the long short-term memory (LSTM) neural network and local smoothing methods to improve the network forecasting model. Moreover, the proposed framework can dynamically react to all the changes occurring in the data series. Backbone traffic was used to validate the proposed method. As a result, the forecasting accuracy improved significantly with the proposed framework and with minimal data loss from the smoothing process. The results showed that the hybrid moving average LSTM (MLSTM) achieved the most remarkable improvement in the training and testing forecasts, with 28% and 24% for long-term evolution (LTE) time series and with 35% and 32% for the multiprotocol label switching (MPLS) time series, respectively, while robust locally weighted scatter plot smoothing and LSTM (RLWLSTM) achieved the most significant improvement for upstream traffic with 45%; moreover, the dynamic learning framework achieved improvement percentages that can reach up to 100%.

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29

Li, Meiyi, and Shengling Cao. "Research on backbone node deployment for Wireless Mesh Networks in dynamic environments." Journal of Physics: Conference Series 887 (August 2017): 012035. http://dx.doi.org/10.1088/1742-6596/887/1/012035.

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30

Noh, Dong Kun, and Junbeom Hur. "Using a dynamic backbone for efficient data delivery in solar-powered WSNs." Journal of Network and Computer Applications 35, no. 4 (July 2012): 1277–84. http://dx.doi.org/10.1016/j.jnca.2012.01.012.

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31

Rahman, Sabidur, Abhishek Gupta, Massimo Tornatore, and Biswanath Mukherjee. "Dynamic Workload Migration Over Backbone Network to Minimize Data Center Electricity Cost." IEEE Transactions on Green Communications and Networking 2, no. 2 (June 2018): 570–79. http://dx.doi.org/10.1109/tgcn.2017.2780133.

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32

Tsuchido, Yoshitaka, Yuji Suzaki, Tomohito Ide, and Kohtaro Osakada. "Dynamic Properties of Molecular Tweezers with a Bis(2-hydroxyphenyl)pyrimidine Backbone." Chemistry - A European Journal 20, no. 16 (March 6, 2014): 4762–71. http://dx.doi.org/10.1002/chem.201304380.

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33

Lei, Zhou, Kangkang Yang, Kai Jiang, and Shengbo Chen. "KDAS-ReID: Architecture Search for Person Re-Identification via Distilled Knowledge with Dynamic Temperature." Algorithms 14, no. 5 (April 26, 2021): 137. http://dx.doi.org/10.3390/a14050137.

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Person re-Identification(Re-ID) based on deep convolutional neural networks (CNNs) achieves remarkable success with its fast speed. However, prevailing Re-ID models are usually built upon backbones that manually design for classification. In order to automatically design an effective Re-ID architecture, we propose a pedestrian re-identification algorithm based on knowledge distillation, called KDAS-ReID. When the knowledge of the teacher model is transferred to the student model, the importance of knowledge in the teacher model will gradually decrease with the improvement of the performance of the student model. Therefore, instead of applying the distillation loss function directly, we consider using dynamic temperatures during the search stage and training stage. Specifically, we start searching and training at a high temperature and gradually reduce the temperature to 1 so that the student model can better learn from the teacher model through soft targets. Extensive experiments demonstrate that KDAS-ReID performs not only better than other state-of-the-art Re-ID models on three benchmarks, but also better than the teacher model based on the ResNet-50 backbone.

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He, Changyu, Zhen Zhang, Qinglai Yang, Qing Chang, Zhifeng Shao, Bing Gong, Yu-Mei Shen, Bingya Liu, and Zhenggang Zhu. "Reductive triblock copolymer micelles with a dynamic covalent linkage deliver antimiR-21 for gastric cancer therapy." Polymer Chemistry 7, no. 26 (2016): 4352–66. http://dx.doi.org/10.1039/c6py00651e.

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35

Shi, Qingsong, Weilin Wu, Bing Yu, Mengqing Ren, Lili Wu, and Chaocan Zhang. "Preparation of ecofriendly water-borne polyurethane elastomer with mechanical robustness and self-healable ability based on multi-dynamic interactions." RSC Advances 12, no. 54 (2022): 35396–408. http://dx.doi.org/10.1039/d2ra07000f.

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Environmentally friendly WPU with multiple hydrogen bonds and boronic ester bonds within its polymer backbone was synthesized. Benefiting from multiple dynamic interactions, the prepared WPU elastomer exhibited good mechanical properties and desirable self-healing ability.

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36

Nishikawa, Yuji, Tatsuhiko Nakano, and Isao Noda. "Two-Dimensional Correlation Analysis of Polyimide Films Using Attenuated Total Reflection-Based Dynamic Compression Modulation Step-Scan Fourier Transform Infrared Spectroscopy." Applied Spectroscopy 61, no. 8 (August 2007): 873–81. http://dx.doi.org/10.1366/000370207781540015.

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Attenuated total reflection (ATR)-based dynamic compression modulation two-dimensional (2D) correlation study of poly(p-phenylene biphenyltetracarboximide) film is carried out in combination with spectral simulation analysis by density functional theory (DFT). The dynamic 2D infrared (IR) correlation spectra in the region of imide I (C=O stretching mode) show three distinct correlation peaks located around 1777, 1725, and 1708 cm−1. The band at 1708 cm−1 is the lower wavenumber shift component of 1777 or 1735 cm−1 peaks and is attributed to the results from intermolecular interactions, according to the DFT analysis. The 1708 cm−1 band also shows the largest dynamic response, suggesting that these intermolecular interactions may enhance the dynamic response. The dynamic 2D IR correlation spectra in the region of imide II (C–N–C axial stretching mode) vibrations also show three correlation peaks located around 1335, 1355, and 1370 cm−1, although the imide II band is shown to consist substantially of one component by the DFT analysis. These multiple peaks may be attributed to the compression-induced wavenumber shift of the band in the backbone structures. The sequential analysis of 2D correlation data show that, upon applying the dynamic compression, the response of the backbone regions (imide II) occurs first, followed by that of the side-chain regions (imide I, C=O).

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37

Song, Hyeong Yong, Lorenz Faust, Jinha Son, Mingeun Kim, Seung Joon Park, Suk-kyun Ahn, Manfred Wilhelm, and Kyu Hyun. "Small and Medium Amplitude Oscillatory Shear Rheology of Model Branched Polystyrene (PS) Melts." Polymers 12, no. 2 (February 7, 2020): 365. http://dx.doi.org/10.3390/polym12020365.

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Linear and nonlinear rheological properties of model comb polystyrenes (PS) with loosely to densely grafted architectures were measured under small and medium amplitude oscillatory shear (SAOS and MAOS) flow. This comb PS set had the same length of backbone and branches but varied in the number of branches from 3 to 120 branches. Linear viscoelastic properties of the comb PS were compared with the hierarchical model predictions. The model underpredicted zero-shear viscosity and backbone plateau modulus of densely branched comb with 60 or 120 branches because the model does not include the effect of side chain crowding. First- and third-harmonic nonlinearities reflected the hierarchy in the relaxation motion of comb structures. Notably, the low-frequency plateau values of first-harmonic MAOS moduli scaled with M w − 2 (total molecular weight), reflecting dynamic tube dilution (DTD) by relaxed branches. Relative intrinsic nonlinearity Q0 exhibited the difference between comb and bottlebrush via no low-frequency Q0 peak of bottlebrush corresponding to backbone relaxation, which is probably related to the stretched backbone conformation in bottlebrush.

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38

Allouzi, Rabab, and Ayhan Irfanoglu. "Development of new nonlinear dynamic response model of reinforced concrete frames with infill walls." Advances in Structural Engineering 21, no. 14 (April 10, 2018): 2154–68. http://dx.doi.org/10.1177/1369433218768915.

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The complex behavior of reinforced concrete frames with infill walls under earthquake loads requires a realistic conceptual model that recognizes changes in strength and stiffness occurring during loading. Accordingly, a new hysteresis model is developed in this article for such reinforced concrete frames to investigate the ultimate damage state given a ground motion. Using this model, the infilled frame can be represented as a single-degree-of-freedom system for computationally efficient dynamic in-plane response analysis. A backbone curve is developed first to provide an envelope within which load–displacement paths occur. Then, the load reversal effects are described and integrated into the backbone curve to obtain the hysteresis model. The hysteresis model developed in this article is checked using data from 11 laboratory experiments carried out by other researchers. The applicability of the hysteresis model is also illustrated on a laboratory specimen that was tested by other researchers under base excitation.

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Schneider, Bohdan, Jean-Christophe Gelly, Alexandre G. de Brevern, and Jiří Černý. "Local dynamics of proteins and DNA evaluated from crystallographicBfactors." Acta Crystallographica Section D Biological Crystallography 70, no. 9 (August 29, 2014): 2413–19. http://dx.doi.org/10.1107/s1399004714014631.

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The dynamics of protein and nucleic acid structures is as important as their average static picture. The local molecular dynamics concealed in diffraction images is expressed as so-calledBfactors. To find out how the crystal-derivedBfactors represent the dynamic behaviour of atoms and residues of proteins and DNA in their complexes, the distributions of scaledBfactors from a carefully curated data set of over 700 protein–DNA crystal structures were analyzed [Schneideret al.(2014),Nucleic Acids Res.42, 3381–3394]. Amino acids and nucleotides were categorized based on their molecular neighbourhood as solvent-accessible, solvent-inaccessible (i.e.forming the protein core) or lying at protein–protein or protein–DNA interfaces; the backbone and side-chain atoms were analyzed separately. TheBfactors of two types of crystal-ordered water molecules were also analyzed. The analysis confirmed several expected features of protein and DNA dynamics, but also revealed surprising facts. Solvent-accessible amino acids haveBfactors that are larger than those of residues at the biomolecular interfaces, and core-forming amino acids are the most restricted in their movement. A unique feature of the latter group is that their side-chain and backbone atoms are restricted in their movement to the same extent; in all other amino-acid groups the side chains are more floppy than the backbone. The low values of theBfactors of water molecules bridging proteins with DNA and the very large fluctuations of DNA phosphates are surprising. The features discriminating different types of residues are less pronounced in structures with lower crystallographic resolution. Some of the observed trends are likely to be the consequence of improper refinement protocols that may need to be rectified.

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Yu, Jianqiang, Xiaomin Dong, Shuaishuai Sun, and Weihua Li. "Comparison of dynamic models based on backbone curve for rotary magneto-rheological damper." Proceedings of the Institution of Mechanical Engineers, Part C: Journal of Mechanical Engineering Science 234, no. 14 (June 11, 2019): 2732–40. http://dx.doi.org/10.1177/0954406219856392.

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To realize the accurate control of magneto-rheological system, the nonlinear dynamic model as the joint of damper and control strategy is worthy of being investigated. In this study, the modeling methods based on the backbone curve are proposed to portray the dynamic characteristics of magneto-rheological damper. The modeling methods contain the phase lag method and the hysteresis division method. Six novel algebraic models are deduced from the two methods and compared systematically. The parameters identification of models is conducted by the nonlinear least square method. The nonlinear least square optimization problem is solved by the Levenberg–Marquardt algorithm. The evaluation indexes including the root-mean-square error, mean deviation and computation time are calculated to evaluate the accuracy and feasibility of the novel models. Results show that the modeling methods and their models can describe the nonlinear hysteretic characteristics with feasibility and accuracy.

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Choi, Won young, Hyunguk Choi, Seo Won Choi, Young Je Park, CHI-Young Jung, Nam Jin Lee, Jong min Lee, and Young Gi Yoon. "The Ionomer Molecular Structure Effect in the PEFC Ink & Applications." ECS Meeting Abstracts MA2022-02, no. 41 (October 9, 2022): 1516. http://dx.doi.org/10.1149/ma2022-02411516mtgabs.

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The interaction between the perfluorosulfonic acid (PFSA) ionomer and platinum group metal (PGM) catalyst in polymer electrolyte fuel cell (PEFC) inks is a critical issue for designing high-performance PEFC electrodes. During the ink fabrication, the complex interparticle interaction of the ink components determines the agglomerate morphology and size distribution. Among the ink components, the ionomer, which has amphiphilic in nature due to its hydrophobic backbone and the hydrophilic ionic group, mostly effective parameter for interparticle interaction. Therefore, understanding the interaction and molecular structure of ionomer is required for a high-performance catalyst layer. The backbone length of the ionomer which controls the spacing between ionic pendant groups is the main parameter of the ionomer character. In this study, the three different ionic spacing ionomers, made in the Solvay industry: Aquivion D72-25BS, Aquivion D83-24BS, and D98-25BS, were used for investigating the adsorption behavior of the catalyst ink and PEFC catalyst layer morphology. During the fabrication of PEFC ink and catalyst layer, all samples have same sulfonic acid molality to avoid the ionic clustering effect in the side chain. Ex-situ measurements were carried out to quantify the interparticle interaction and agglomerate size distribution in the PEFC ink. The dynamic lights scattering (DLS) carry out to determine the aggregation size distribution. The rheological behavior was conducted to understand the interparticle interactions and the agglomeration behavior of the inks by steady-shear and dynamic-oscillatory-shear measurements. It is noted that increasing the ionomer backbone length, which favors interaction via hydrophobic interaction on a carbon support, suppresses the agglomeration of ink components and decreases ink viscosity. The in situ electrochemical tests were carried out to figure out the relationship between ink formulation and catalyst layer morphology. It was found that the long ionomer backbone length helps to suppress the O2 transport resistance and ORR kinetic loss by uniform distribution from ionomer backbone-carbon supports interaction.

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Urushidani, Shigeo, Kensuke Fukuda, Michihiro Koibuchi, Motonori Nakamura, Shunji Abe, Yusheng Ji, Michihiro Aoki, and Shigeki Yamada. "Dynamic Resource Allocation and QoS Control Capabilities of the Japanese Academic Backbone Network." Future Internet 2, no. 3 (August 9, 2010): 295–307. http://dx.doi.org/10.3390/fi2030295.

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Yu, Xiaosong, Jiye Wang, Kaixin Zhang, Jiaqi Lv, Yongli Zhao, Kaiqiang Gao, Xuerang Guo, and Jie Zhang. "Brown-Field Migration Aware Routing and Spectrum Assignment in Backbone Optical Networks." Applied Sciences 12, no. 1 (January 3, 2022): 438. http://dx.doi.org/10.3390/app12010438.

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With the development of optical networks technology, broad attention has been paid to flexible grid technology in optical networks due to its ability to carry large-capacity information as well as provide flexible and fine-grained services through on-demand spectrum resource allocation. However, a one-time green-field deployment of a flexible grid network may not be practical. The transition technology called the fixed/flex-grid optical networks is more applicable and highly pragmatic. In such network, many nodes would likely be upgraded from a fixed-grid to flex-grid. In fact, dynamic service provisioning during the process of a node upgrade in fixed/flex-grid optical networks have become a challenge because the service connection can be easily interrupted, which leads to considerable data loss because of node upgrade. To overcome this challenge, we propose a brown-field migration aware routing and spectrum assignment (BMA-RSA) algorithm in fixed/flex-grid optical networks. The aim is to construct a probabilistic migration label (PML) model. The well-designed label setting of PML can balance the relationship between distance and node-upgrade probability. Dynamic service provisioning operations are undertaken based on the PML model to achieve a migration-aware dynamic connection before network migration occurs. We also evaluate the performance of different service provisioning strategies under different traffic models. The simulation results show that the BMA-RSA algorithm can achieve: (1) the tradeoff between distance and node upgrade probability during the process of service provisioning; (2) lower service interruption compared with the traditional non-migration aware K-shortest-path routing and spectrum assignment algorithm.

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Tumiran, Lesnanto Multa Putranto, Roni Irnawan, Sarjiya, Adi Priyanto, Suroso Isnandar, and Ira Savitri. "Transmission Expansion Planning for the Optimization of Renewable Energy Integration in the Sulawesi Electricity System." Sustainability 13, no. 18 (September 21, 2021): 10477. http://dx.doi.org/10.3390/su131810477.

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In order to meet the growth in demand and the renewable energy integration target, the Sulawesi Electricity System (SES) should be expanded. Currently, the SES is divided into two systems, namely South and North Sulawesi. These two systems have different characteristics, such as the system size, reliability and operational cost. North Sulawesi is smaller, weaker and more expensive than the South System. In order to improve the system reliability, generation and transmission expansion planning should be executed simultaneously to meet the economical investment cost and satisfy the reliability standard. For this purpose, the necessity of a backbone system with a higher voltage level than the existing 150 kV system should be considered, including the interconnection option between the two existing systems in Sulawesi. A methodology based on economic and technical criteria was developed to determine the backbone voltage level. Two voltage level options were considered, namely 275 and 500 kV. Several criteria were considered in order to determine the backbone voltage level, including the economic voltage, the line-loading limit, N-1 contingency, short circuiting, transient stability, voltage stability and small signal stability. The backbone voltage candidates should fulfil all of the criteria. The simulation was conducted in base- and high-demand scenarios, considering the fluctuation of future economic growth. The load flow and the dynamic analysis were simulated in a DIgSILENT Power Factory environment. The results showed that the 275 kV backbone, which was built in 2022, would violate three criteria: the economic voltage, N-1 contingency and voltage stability. On the other hand, the 500 kV backbone voltage level fulfills all of the criteria. The result of this research was considered in the electricity planning documents in Sulawesi. From a technical and economical perspective, the 500 kV backbone was chosen for the SES.

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Hu, Zhongjian, Ryan T. Haws, Zhuping Fei, Pierre Boufflet, Martin Heeney, Peter J. Rossky, and David A. Vanden Bout. "Impact of backbone fluorination on nanoscale morphology and excitonic coupling in polythiophenes." Proceedings of the National Academy of Sciences 114, no. 20 (May 2, 2017): 5113–18. http://dx.doi.org/10.1073/pnas.1620722114.

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Fluorination represents an important strategy in developing high-performance conjugated polymers for photovoltaic applications. Here, we use regioregular poly(3-ethylhexylthiophene) (P3EHT) and poly(3-ethylhexyl-4-fluorothiophene) (F-P3EHT) as simplified model materials, using single-molecule/aggregate spectroscopy and molecular dynamic simulations, to elucidate the impacts of backbone fluorination on morphology and excitonic coupling on the molecular scale. Despite its high regioregularity, regioregular P3EHT exhibits a rather broad distribution in polymer chain conformation due to the strong steric hindrance of bulky ethylhexyl side chains. This conformational variability results in disordered interchain morphology even between a few chains, prohibiting long-range effective interchain coupling. In stark contrast, the experimental and molecular dynamic calculations reveal that backbone fluorination of F-P3EHT leads to an extended rod-like single-chain conformation and hence highly ordered interchain packing in aggregates. Surprisingly, the ordered and close interchain packing in F-P3EHT does not lead to strong excitonic coupling between the chains but rather to dominant intrachain excitonic coupling that greatly reduces the molecular energetic heterogeneity.

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Jiao, Wanting, Yifei Fan, Nicola J. Blackmore, and Emily J. Parker. "A single amino acid substitution uncouples catalysis and allostery in an essential biosynthetic enzyme in Mycobacterium tuberculosis." Journal of Biological Chemistry 295, no. 19 (March 26, 2020): 6252–62. http://dx.doi.org/10.1074/jbc.ra120.012605.

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Allostery exploits the conformational dynamics of enzymes by triggering a shift in population ensembles toward functionally distinct conformational or dynamic states. Allostery extensively regulates the activities of key enzymes within biosynthetic pathways to meet metabolic demand for their end products. Here, we have examined a critical enzyme, 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (DAH7PS), at the gateway to aromatic amino acid biosynthesis in Mycobacterium tuberculosis, which shows extremely complex dynamic allostery: three distinct aromatic amino acids jointly communicate occupancy to the active site via subtle changes in dynamics, enabling exquisite fine-tuning of delivery of these essential metabolites. Furthermore, this allosteric mechanism is co-opted by pathway branchpoint enzyme chorismate mutase upon complex formation. In this study, using statistical coupling analysis, site-directed mutagenesis, isothermal calorimetry, small-angle X-ray scattering, and X-ray crystallography analyses, we have pinpointed a critical node within the complex dynamic communication network responsible for this sophisticated allosteric machinery. Through a facile Gly to Pro substitution, we have altered backbone dynamics, completely severing the allosteric signal yet remarkably, generating a nonallosteric enzyme that retains full catalytic activity. We also identified a second residue of prime importance to the inter-enzyme communication with chorismate mutase. Our results reveal that highly complex dynamic allostery is surprisingly vulnerable and provide further insights into the intimate link between catalysis and allostery.

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Yang, Min June, Jinwoo Kim, Yeongjoon Lee, Woonghee Lee, and Chin-Ju Park. "NMR Structure and Biophysical Characterization of Thermophilic Single-Stranded DNA Binding Protein from Sulfolobus Solfataricus." International Journal of Molecular Sciences 23, no. 6 (March 13, 2022): 3099. http://dx.doi.org/10.3390/ijms23063099.

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Proteins from Sulfolobus solfataricus (S. solfataricus), an extremophile, are active even at high temperatures. The single-stranded DNA (ssDNA) binding protein of S. solfataricus (SsoSSB) is overexpressed to protect ssDNA during DNA metabolism. Although SsoSSB has the potential to be applied in various areas, its structural and ssDNA binding properties at high temperatures have not been studied. We present the solution structure, backbone dynamics, and ssDNA binding properties of SsoSSB at 50 °C. The overall structure is consistent with the structures previously studied at room temperature. However, the loop between the first two β sheets, which is flexible and is expected to undergo conformational change upon ssDNA binding, shows a difference from the ssDNA bound structure. The ssDNA binding ability was maintained at high temperature, but different interactions were observed depending on the temperature. Backbone dynamics at high temperature showed that the rigidity of the structured region was well maintained. The investigation of an N-terminal deletion mutant revealed that it is important for maintaining thermostability, structure, and ssDNA binding ability. The structural and dynamic properties of SsoSSB observed at high temperature can provide information on the behavior of proteins in thermophiles at the molecular level and guide the development of new experimental techniques.

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Sun, Shengtong, and Peiyi Wu. "Conformational changes in the heat-induced crystallization of poly(2-isopropyl-2-oxazoline) in the solid state." Physical Chemistry Chemical Physics 17, no. 46 (2015): 31084–92. http://dx.doi.org/10.1039/c5cp05719a.

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The dynamic solid-state crystallization process of poly(2-isopropyl-2-oxazoline) was studied by vibrational spectroscopy in combination with two-dimensional correlation analysis, and is shown to be mainly achieved by the lateral distortion of coplanar side chains together with the torsion of the backbone through C–N linkages.

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Radić, Zoran. "Shifts in Backbone Conformation of Acetylcholinesterases upon Binding of Covalent Inhibitors, Reversible Ligands and Substrates." Crystals 11, no. 12 (December 14, 2021): 1557. http://dx.doi.org/10.3390/cryst11121557.

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The influence of ligand binding to human, mouse and Torpedo californica acetylcholinesterase (EC 3.1.1.7; AChE) backbone structures is analyzed in a pairwise fashion by comparison with X-ray structures of unliganded AChEs. Both complexes with reversible ligands (substrates and inhibitors) as well as covalently interacting ligands leading to the formation of covalent AChE conjugates of tetrahedral and of trigonal-planar geometries are considered. The acyl pocket loop (AP loop) in the AChE backbone is recognized as the conformationally most adaptive, but not necessarily sterically exclusive, structural element. Conformational changes of the centrally located AP loop coincide with shifts in C-terminal α-helical positions, revealing interacting components for a potential allosteric interaction within the AChE backbone. The stabilizing power of the aromatic choline binding site, with the potential to attract and pull fitting entities covalently tethered to the active Ser, is recognized. Consequently, the pull can promote catalytic reactions or relieve steric pressure within the impacted space of the AChE active center gorge. These dynamic properties of the AChE backbone inferred from the analysis of static X-ray structures contribute towards a better understanding of the molecular template important in the structure-based design of therapeutically active molecules, including AChE inhibitors as well as reactivators of conjugated, inactive AChE.

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Kanlidere, Zeynep, Oleg Jochim, Marta Cal, and Ulf Diederichsen. "DNA functionalization by dynamic chemistry." Beilstein Journal of Organic Chemistry 12 (October 6, 2016): 2136–44. http://dx.doi.org/10.3762/bjoc.12.203.

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Dynamic combinatorial chemistry (DCC) is an attractive method to efficiently generate libraries of molecules from simpler building blocks by reversible reactions under thermodynamic control. Here we focus on the chemical modification of DNA oligonucleotides with acyclic diol linkers and demonstrate their potential for the deoxyribonucleic acid functionalization and generation of libraries of reversibly interconverting building blocks. The syntheses of phosphoramidite building blocks derived from D-threoninol are presented in two variants with protected amino or thiol groups. The threoninol building blocks were successfully incorporated via automated solid-phase synthesis into 13mer oligonucleotides. The amino group containing phosphoramidite was used together with complementary single-strand DNA templates that influenced the Watson–Crick base-pairing equilibrium in the mixture with a set of aldehyde modified nucleobases. A significant fraction of all possible base-pair mismatches was obtained, whereas, the highest selectivity (over 80%) was found for the guanine aldehyde templated by the complementary cytosine containing DNA. The elevated occurrence of mismatches can be explained by increased backbone plasticity derived from the linear threoninol building block as a cyclic deoxyribose analogue.

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