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Journal articles on the topic 'Biomolecular system'

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Author: Grafiati

Published: 14 March 2023

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1

Raković, Dejan, Miroljub Dugić, Jasmina Jeknić-Dugić, Milenko Plavšić, Stevo Jaćimovski, and Jovan Šetrajčić. "On Macroscopic Quantum Phenomena in Biomolecules and Cells: From Levinthal to Hopfield." BioMed Research International 2014 (2014): 1–9. http://dx.doi.org/10.1155/2014/580491.

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In the context of the macroscopic quantum phenomena of the second kind, we hereby seek for a solution-in-principle of the long standing problem of the polymer folding, which was considered by Levinthal as (semi)classically intractable. To illuminate it, we applied quantum-chemical and quantum decoherence approaches to conformational transitions. Our analyses imply the existence of novel macroscopic quantum biomolecular phenomena, with biomolecular chain folding in an open environment considered as a subtle interplay between energy and conformation eigenstates of this biomolecule, governed by quantum-chemical and quantum decoherence laws. On the other hand, within an open biological cell, a system of all identical (noninteracting and dynamically noncoupled) biomolecular proteins might be considered as corresponding spatial quantum ensemble of these identical biomolecular processors, providing spatially distributed quantum solution to a single corresponding biomolecular chain folding, whose density of conformational states might be represented as Hopfield-like quantum-holographic associative neural network too (providing an equivalent global quantum-informational alternative to standard molecular-biology local biochemical approach in biomolecules and cells and higher hierarchical levels of organism, as well).

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2

Hong, Yoochan, Yong-Min Huh, Dae Sung Yoon, and Jaemoon Yang. "Nanobiosensors Based on Localized Surface Plasmon Resonance for Biomarker Detection." Journal of Nanomaterials 2012 (2012): 1–13. http://dx.doi.org/10.1155/2012/759830.

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Localized surface plasmon resonance (LSPR) is induced by incident light when it interacts with noble metal nanoparticles that have smaller sizes than the wavelength of the incident light. Recently, LSPR-based nanobiosensors were developed as tools for highly sensitive, label-free, and flexible sensing techniques for the detection of biomolecular interactions. In this paper, we describe the basic principles of LSPR-based nanobiosensing techniques and LSPR sensor system for biomolecule sensing. We also discuss the challenges using LSPR nanobiosensors for detection of biomolecules as a biomarker.

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3

Gawthrop, Peter. "Computing Biomolecular System Steady-States." IEEE Transactions on NanoBioscience 17, no. 1 (January 2018): 36–43. http://dx.doi.org/10.1109/tnb.2017.2787486.

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4

Fujisaki, Hiroshi, Kei Moritsugu, and Yasuhiro Matsunaga. "Exploring Configuration Space and Path Space of Biomolecules Using Enhanced Sampling Techniques—Searching for Mechanism and Kinetics of Biomolecular Functions." International Journal of Molecular Sciences 19, no. 10 (October 15, 2018): 3177. http://dx.doi.org/10.3390/ijms19103177.

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To understand functions of biomolecules such as proteins, not only structures but their conformational change and kinetics need to be characterized, but its atomistic details are hard to obtain both experimentally and computationally. Here, we review our recent computational studies using novel enhanced sampling techniques for conformational sampling of biomolecules and calculations of their kinetics. For efficiently characterizing the free energy landscape of a biomolecule, we introduce the multiscale enhanced sampling method, which uses a combined system of atomistic and coarse-grained models. Based on the idea of Hamiltonian replica exchange, we can recover the statistical properties of the atomistic model without any biases. We next introduce the string method as a path search method to calculate the minimum free energy pathways along a multidimensional curve in high dimensional space. Finally we introduce novel methods to calculate kinetics of biomolecules based on the ideas of path sampling: one is the Onsager–Machlup action method, and the other is the weighted ensemble method. Some applications of the above methods to biomolecular systems are also discussed and illustrated.

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Hradetzky, David, Claas Mueller, and Holger Reinecke. "Interferometric label-free biomolecular detection system." Journal of Optics A: Pure and Applied Optics 8, no. 7 (June 1, 2006): S360—S364. http://dx.doi.org/10.1088/1464-4258/8/7/s11.

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6

Leinen, Margaret, Francisco Chavez, Raïssa Meyer, Pier Luigi Buttigieg, Neil Davies, Raffaella Casotti, and Astrid Fischer. "The Ocean Biomolecular Observing Network (OBON)." Marine Technology Society Journal 56, no. 3 (June 8, 2022): 106–7. http://dx.doi.org/10.4031/mtsj.56.3.20.

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Abstract Ocean life—from viruses to whales—is built from “biomolecules.” Biomolecules such as DNA infuse each drop of ocean water, grain of sediment, and breath of ocean air. The Ocean Biomolecular Observing Network (OBON) is developing a global collaboration that will allow science and society to understand ocean life like never before. The program will transform how we sense, harvest, protect, and manage ocean life using molecular techniques, as it faces multiple stresses including pollution, habitat loss, and climate change. It will also help communities detect biological hazards such as harmful algal blooms and pathogens, and be a key component of next-generation ocean observing systems. OBON will encourage continuous standardization and intercalibration of methods and data interoperability to help enhance and future-proof capabilities. OBON's objectives are: 1) to build a coastal-to-open ocean multi-omics biodiversity observing system; 2) to develop and transfer capacity between partners; 3) to enhance marine ecosystem digitization and modelling and 4) to coordinate action on pressing scientific, management, and policy questions.

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7

Yokokawa, R., S. Takeuchi, T. Kon, M. Nishiura, R. Ohkura, M. Edamatsu, K. Sutoh, and H. Fujita. "Hybrid Nanotransport System by Biomolecular Linear Motors." Journal of Microelectromechanical Systems 13, no. 4 (August 2004): 612–19. http://dx.doi.org/10.1109/jmems.2004.832193.

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8

Ishii, Takahiro, Mitsunori Ikeguchi, Toshihiro Yamada, and Junta Doi. "Development of interactive biomolecular graphics system LIVE." Journal of Molecular Graphics 10, no. 1 (March 1992): 48–49. http://dx.doi.org/10.1016/0263-7855(92)80026-a.

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9

Xuan, G., S. Ghosh, S. Kim, P.-C. Lv, T. Buma, B. Weng, K. Barner, and J. Kolodzey. "TERAHERTZ SENSING OF MATERIALS." International Journal of High Speed Electronics and Systems 17, no. 01 (March 2007): 121–26. http://dx.doi.org/10.1142/s0129156407004333.

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Biomolecules such as DNA and proteins exhibit a wealth of modes in the Terahertz (THz) range from the rotational, vibrational and stretching modes of biomolecules. Many materials such as drywall that are opaque to human eyes are transparent to THz. Therefore, it can be used as a powerful tool for biomolecular sensing, biomedical analysis and through-the-wall imaging. Experiments were carried out to study the absorption of various materials including DNA and see-through imaging of drywall using FTIR spectrometer and Time Domain Spectroscopy (TDS) system.

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10

David A Dawson and Clare P Persad. "Targeting the endocannabinoid system in the treatment of addiction disorders." GSC Biological and Pharmaceutical Sciences 19, no. 2 (May 30, 2022): 064–74. http://dx.doi.org/10.30574/gscbps.2022.19.2.0175.

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This disquisition provides historical context illustrating the psychosocial, political, and bureaucratic barriers to applying a biomolecular approach to substance use disorders, focusing on what are arguably the most stigmatized molecules in America. It provides a biomolecular treatment strategy designed to mitigate multiple types of addiction by influencing the dopamine and serotonin neurotransmitters’ activity through phytocannabinoid supplementation of the endocannabinoid system and proposes a strategy for circumventing the bureaucratic obstacles.

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11

Raković, D., M. Dugić, M. B. Plavšić, G. Keković, Irena Ćosić, and David Davidović. "Quantum Decoherence and Quantum-Holographic Information Processes: From Biomolecules to Biosystems." Materials Science Forum 518 (July 2006): 485–90. http://dx.doi.org/10.4028/www.scientific.net/msf.518.485.

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Our recently proposed quantum approach to biomolecular recognition processes is hereby additionally supported by biomolecular Resonant Recognition Model and by quantum-chemical theory of biomolecular non-radiative resonant transitions. Previously developed general quantumdecoherence framework for biopolymer conformational changes in very selective ligandproteins/ target-receptors key/lock biomolecular recognition processes (with electron-conformational coupling, giving rise to dynamical modification of many-electron energy-state hypersurface of the cellular quantum-ensemble ligand-proteins/target-receptors biomolecular macroscopic quantum system, with revealed possibility to consider cellular biomolecular recognition as a Hopfield-like quantum-holographic associative neural network) is further extended from nonlocal macroscopicquantum level of biological cell to nonlocal macroscopic-quantum level of biological organism, based on long-range coherent microwave excitations (as supported by macroscopic quantum-like microwave resonance therapy of the acupuncture system) - which might be of fundamental importance in understanding of underlying macroscopic quantum (quantum-holographic Hopfieldlike) control mechanisms of embryogenesis/ontogenesis and morphogenesis, and their backward influence on the expression of genes.

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12

Kim, Sang-Gyu, Hee-Jo Lee, and Jong-Gwan Yook. "A Biomolecular Sensing Platform Using RF Active System." Journal of electromagnetic engineering and science 12, no. 4 (December 31, 2012): 227–33. http://dx.doi.org/10.5515/jkiees.2012.12.4.227.

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13

Noe, Christian, Jerome Freissmuth, Peter Richter, Christian Miculka, Bodo Lachmann, and Simon Eppacher. "Formaldehyde—A Key Monad of the Biomolecular System." Life 3, no. 3 (August 16, 2013): 486–501. http://dx.doi.org/10.3390/life3030486.

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14

Sjoelander, Stefan, and Csaba Urbaniczky. "Integrated fluid handling system for biomolecular interaction analysis." Analytical Chemistry 63, no. 20 (October 15, 1991): 2338–45. http://dx.doi.org/10.1021/ac00020a025.

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15

Schmitt, Hans-Martin, Andreas Brecht, Jacob Piehler, and Günter Gauglitz. "An integrated system for optical biomolecular interaction analysis." Biosensors and Bioelectronics 12, no. 8 (July 1997): 809–16. http://dx.doi.org/10.1016/s0956-5663(97)00046-8.

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16

Yokokawa, R., S. Takeuchi, T. Kon, M. Nishiura, K. Sutoh, and H. Fujita. "Control of Biomolecular Motors for Nano Transfer System." Proceedings of JSME annual Conference on Robotics and Mechatronics (Robomec) 2003 (2003): 116. http://dx.doi.org/10.1299/jsmermd.2003.116_3.

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17

Mrozowich, Tyler, Vanessa MeierStephenson, and Trushar R. Patel. "Microscale thermophoresis: warming up to a new biomolecular interaction technique." Biochemist 41, no. 2 (April 1, 2019): 8–12. http://dx.doi.org/10.1042/bio04102008.

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Biomolecules, such as RNA, DNA, proteins and polysaccharides, are at the heart of fundamental cellular processes. These molecules differ greatly with each other in terms of their structures and functions. However, in the midst of the diversity of biomolecules is the unifying feature that they interact with each other to execute a viable biological system. Interactions of biomolecules are critical for cells to survive and replicate, for food metabolism to produce energy, for antibiotics and vaccines to function, for spreading of diseases and for every other biological process. An improved understanding of these interactions is crucial for studying how cells and organs function, to appreciate how diseases are caused and how infections occur, with infinite implications in medicine and therapy. Many biochemical and biophysical techniques are currently being employed to study biomolecular interactions. Microscale thermophoresis (MST) is a relatively new biophysical technique that can provide powerful insight into the interactions of biomolecules and is quickly being adopted by an increasing number of researchers worldwide. This article provides a brief description of principles underpinning the MST process, in addition to benefits and limitations.

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18

Wulandari, Patricia. "Biomolecular Aspects of Schizophrenia." Bioscientia Medicina : Journal of Biomedicine and Translational Research 3, no. 2 (May 30, 2019): 38–43. http://dx.doi.org/10.32539/bsm.v3i2.88.

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Abstract Schizophrenia is a common psychiatric disorder, which is characterized by severe distortion of reality; disturbances in thoughts, feelings and behavior; according to DSM V is a disorder form deviations fundamentals and characteristics of thought and perception, and by the innapropriate or blunted affect. The influence of genetics is believed to have a role in psychiatric disorders, especially if the disorder has occurred in young adults or adolescents. The pathophysiology of schizophrenia is closely related to disorders of the biomolecular aspects of the central nervous system. Dopamine activity in the striatal area and prefrontal cortex is a mechanism believed to be the cause of the emergence of positive and negative symptoms in schizophrenia. Meanwhile, neuronal cell apoptosis and increased oxidants, especially in the basal ganglia and prefrontal cortex areas cause worsening of negative symptoms experienced by schizophrenic patients.

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19

Luan, Chonglin, Haipei Luan, and Dawei Luo. "Application and Technique of Liquid Crystal-Based Biosensors." Micromachines 11, no. 2 (February 8, 2020): 176. http://dx.doi.org/10.3390/mi11020176.

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Liquid crystal biosensors are based on changes in the orientation of liquid crystal molecules induced by specific bonding events of biomolecules. These biosensors are expected to serve as a promising system to detect biomolecules, biomolecular activity, and even small chemical molecules because they are inexpensive, sensitive, simple, effective, and portable. Herein, we introduce the principle and fabrication of liquid crystal biosensors and review the research progress in signal-amplified technology for liquid crystal sensing and its application in the detection of viruses, bacteria, proteins, nucleic acids, and small chemical molecules. In addition, the current theoretical and practical issues related to liquid crystal biosensors were investigated.

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20

Oohashi, Tsutomu, Osamu Ueno, Tadao Maekawa, Norie Kawai, Emi Nishina, and Manabu Honda. "An Effective Hierarchical Model for the Biomolecular Covalent Bond: An Approach Integrating Artificial Chemistry and an Actual Terrestrial Life System." Artificial Life 15, no. 1 (January 2009): 29–58. http://dx.doi.org/10.1162/artl.2009.15.1.15103.

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Under the AChem paradigm and the programmed self-decomposition (PSD) model, we propose a hierarchical model for the biomolecular covalent bond (HBCB model). This model assumes that terrestrial organisms arrange their biomolecules in a hierarchical structure according to the energy strength of their covalent bonds. It also assumes that they have evolutionarily selected the PSD mechanism of turning biological polymers (BPs) into biological monomers (BMs) as an efficient biomolecular recycling strategy. We have examined the validity and effectiveness of the HBCB model by coordinating two complementary approaches: biological experiments using existent terrestrial life, and simulation experiments using an AChem system. Biological experiments have shown that terrestrial life possesses a PSD mechanism as an endergonic, genetically regulated process and that hydrolysis, which decomposes a BP into BMs, is one of the main processes of such a mechanism. In simulation experiments, we compared different virtual self-decomposition processes. The virtual species in which the self-decomposition process mainly involved covalent bond cleavage from a BP to BMs showed evolutionary superiority over other species in which the self-decomposition process involved cleavage from BP to classes lower than BM. These converging findings strongly support the existence of PSD and the validity and effectiveness of the HBCB model.

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21

Okere, Osheke Shekins, Moses Dele Adams, and Chinazo Glory Orji. "Chemical composition, in vivo immunomodulatory and anti-hyperlipidaemic properties of Rhinoceros (Rhino) oil in lead-induced immunocompromised models." Journal of Phytomedicine and Therapeutics 21, no. 2 (December 5, 2022): 931–74. http://dx.doi.org/10.4314/jopat.v21i2.15.

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A knowledge of the chemical content of Rhinoceros (Rhino) oil and its activity on selected biomolecules of experimental models would help boost the immune system against an immunocompromised COVID-19 status. The study seeks to evaluate the chemical and biomolecular profile of Rhino oil. Chemical profile was done using standard methods of analysis. 25 rats were assigned in five groups (A-E) (n=5). Animals in group A (control) were administered 0.5 ml of distilled water while those in groups B-E which were immunocompromised (by intraperitoneal administration of 5 mg/kg body weight (b.w) of lead [Pb]) were also administered distilled water, immunomodulatory drug (5 mg/kg body weight of zinc [Zn]), 2 and 5 mg/kg b.w of Rhino oil extract respectively, once daily for 8 days followed by biomolecular assay. Proximate analysis gave moisture content (14.37±0.29), among others. FAMEs analysis showed hexadecanoic acid (12.80%) and other esters. Lipid profile of the oil gave LDLC to contain (32.90±0.53 mg/L), and others. The physicochemical properties gave iodine value as (115.80±0.40 mg/g), among others. The metal composition revealed Zn (0.28±0.06) plus others. The amnio acid profile of the oil gave ten essential amino acids and non-essential amino acids respectively. The levels of biomolecules in serum of the animals were altered at specific doses of the oil extract. Altogether, the chemical content of the oil was significantly high, with altered biomolecular effect. The rich content of vital nutrients and chemicals of Rhino oil may boost the white blood cells against COVID-19. The isolation and characterization of the active principles of the oil is encouraged.

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22

Okunoye Ba, O. "Modeling the Distribution of Primes in a Biomolecular System." Research Journal of Applied Sciences 6, no. 4 (April 1, 2011): 258–60. http://dx.doi.org/10.3923/rjasci.2011.258.260.

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23

LIU, Wei-Chiun, Bin-Da LIU, and Chia-Ling WEI. "A Multi-Channel Electrochemical Measurement System for Biomolecular Detection." IEICE Transactions on Electronics E99.C, no. 11 (2016): 1295–303. http://dx.doi.org/10.1587/transele.e99.c.1295.

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24

Lin, Chie-Chieh, Fu-Hsiang Ko, Chun-Chi Chen, Yuh-Shyong Yang, Feng-Chi Chang, and Chung-Shu Wu. "Miniaturized metal semiconductor metal photocurrent system for biomolecular sensingviachemiluminescence." ELECTROPHORESIS 30, no. 18 (September 2009): 3189–97. http://dx.doi.org/10.1002/elps.200900120.

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25

Freymond, Chantal V., Nicole Kündig, Courcelle Stark, Francien Peterse, Björn Buggle, Maarten Lupker, Michael Plötze, et al. "Evolution of biomolecular loadings along a major river system." Geochimica et Cosmochimica Acta 223 (February 2018): 389–404. http://dx.doi.org/10.1016/j.gca.2017.12.010.

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26

Choy, Jin Ho. "Biological Hybrid Materials for Drug Delivery System." Solid State Phenomena 111 (April 2006): 1–6. http://dx.doi.org/10.4028/www.scientific.net/ssp.111.1.

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We have attempted to realize new biomolecular-inorganic nanohybrids with two different functions, one from inorganic moiety and the other from biological one. Recently we were quite successful in demonstrating that a two-dimensional inorganic compound like layered double hydroxide (LDH) can be used as gene or drug delivery carriers. Such inorganic vectors are completely new and different from conventionally developed ones such as viral-based, naked, and cationic liposomes, those which are limited in certain cases of applications due to their toxicity, immunogenecity, poor integration, and etc. But the mentioned problems can be overcome by synthesizing inorganic vectors properly with non-toxic metal ions having biological compatibility. Since LDHs with positive layer charge have an anion exchange capacity, functional biomolecules with a negative charge can be intercalated into hydroxide layers of LDH by a simple ion-exchange reaction to form a bio-LDH nanohybrid. We also found that the hydroxide layers of LDHs could protect the intercalated molecules very efficiently. If necessary, inorganic materials, as reservoir and delivery carrier, can be intentionally removed by dissolving it in an acidic which offer a way of recovering the encapsulated biomolecules. The possible roles of inorganic lattice as the gene and drug delivery carrier will be shown by demonstrating the cellular uptake experiments of FITC, fluorophore, with laser scanning confocal fluorescence microscopy. A

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27

Amzallag, Emmanuel, and Eran Hornstein. "Crosstalk between Biomolecular Condensates and Proteostasis." Cells 11, no. 15 (August 4, 2022): 2415. http://dx.doi.org/10.3390/cells11152415.

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Proper homeostasis of the proteome, referred to as proteostasis, is maintained by chaperone-dependent refolding of misfolded proteins and by protein degradation via the ubiquitin-proteasome system and the autophagic machinery. This review will discuss a crosstalk between biomolecular condensates and proteostasis, whereby the crowding of proteostasis factors into macromolecular assemblies is often established by phase separation of membraneless biomolecular condensates. Specifically, ubiquitin and other posttranslational modifications come into play as agents of phase separation, essential for the formation of condensates and for ubiquitin-proteasome system activity. Furthermore, an intriguing connection associates malfunction of the same pathways to the accumulation of misfolded and ubiquitinated proteins in aberrant condensates, the formation of protein aggregates, and finally, to the pathogenesis of neurodegenerative diseases. The crosstalk between biomolecular condensates and proteostasis is an emerging theme in cellular and disease biology and further studies will focus on delineating specific molecular pathways involved in the pathogenesis of amyotrophic lateral sclerosis (ALS) and other neurodegenerative diseases.

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28

Fratto, Brian E., Nataliia Guz, and Evgeny Katz. "Biomolecular Computing Realized in Parallel Flow Systems: Enzyme-Based Double Feynman Logic Gate." Parallel Processing Letters 25, no. 01 (March 2015): 1540001. http://dx.doi.org/10.1142/s0129626415400010.

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An enzyme system organized in a flow device with three parallel channels was used to mimic a reversible Double Feynman Gate (DFG) with three input and three output signals. Reversible conversion of NAD+ and NADH cofactors was used to perform XOR logic operations, while biocatalytic oxidation of NADH resulted in Identity operation working in parallel. The first biomolecular realization of a DFG gate is promising for integrating into complex biomolecular networks operating in future unconventional biocomputing systems, as well as for novel biosensor applications.

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29

Perlasca, Paolo, Marco Frasca, Cheick Tidiane Ba, Jessica Gliozzo, Marco Notaro, Mario Pennacchioni, Giorgio Valentini, and Marco Mesiti. "Multi-resolution visualization and analysis of biomolecular networks through hierarchical community detection and web-based graphical tools." PLOS ONE 15, no. 12 (December 22, 2020): e0244241. http://dx.doi.org/10.1371/journal.pone.0244241.

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The visual exploration and analysis of biomolecular networks is of paramount importance for identifying hidden and complex interaction patterns among proteins. Although many tools have been proposed for this task, they are mainly focused on the query and visualization of a single protein with its neighborhood. The global exploration of the entire network and the interpretation of its underlying structure still remains difficult, mainly due to the excessively large size of the biomolecular networks. In this paper we propose a novel multi-resolution representation and exploration approach that exploits hierarchical community detection algorithms for the identification of communities occurring in biomolecular networks. The proposed graphical rendering combines two types of nodes (protein and communities) and three types of edges (protein-protein, community-community, protein-community), and displays communities at different resolutions, allowing the user to interactively zoom in and out from different levels of the hierarchy. Links among communities are shown in terms of relationships and functional correlations among the biomolecules they contain. This form of navigation can be also combined by the user with a vertex centric visualization for identifying the communities holding a target biomolecule. Since communities gather limited-size groups of correlated proteins, the visualization and exploration of complex and large networks becomes feasible on off-the-shelf computer machines. The proposed graphical exploration strategies have been implemented and integrated in UNIPred-Web, a web application that we recently introduced for combining the UNIPred algorithm, able to address both integration and protein function prediction in an imbalance-aware fashion, with an easy to use vertex-centric exploration of the integrated network. The tool has been deeply amended from different standpoints, including the prediction core algorithm. Several tests on networks of different size and connectivity have been conducted to show off the vast potential of our methodology; moreover, enrichment analyses have been performed to assess the biological meaningfulness of detected communities. Finally, a CoV-human network has been embedded in the system, and a corresponding case study presented, including the visualization and the prediction of human host proteins that potentially interact with SARS-CoV2 proteins.

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Yang, Ying, and Benzhuo Lu. "An Error Analysis for the Finite Element Approximation to the Steady-State Poisson-Nernst-Planck Equations." Advances in Applied Mathematics and Mechanics 5, no. 1 (February 2013): 113–30. http://dx.doi.org/10.4208/aamm.11-m11184.

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AbstractPoisson-Nernst-Planck equations are a coupled system of nonlinear partial differential equations consisting of the Nernst-Planck equation and the electrostatic Poisson equation with delta distribution sources, which describe the electrodiffusion of ions in a solvated biomolecular system. In this paper, some error bounds for a piecewise finite element approximation to this problem are derived. Several numerical examples including biomolecular problems are shown to support our analysis.

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31

Gribkova, Irina N., Michail N. Eliseev, Yuri D. Belkin, Maxim A. Zakharov, and Olga A. Kosareva. "The Influence of Biomolecule Composition on Colloidal Beer Structure." Biomolecules 12, no. 1 (December 24, 2021): 24. http://dx.doi.org/10.3390/biom12010024.

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Recent studies have revealed an interest in the composition of beer biomolecules as a colloidal system and their influence on the formation of beer taste. The purpose of this research was to establish biochemical interactions between the biomolecules of plant-based raw materials of beer in order to understand the overall structure of beer as a complex system of bound biomolecules. Generally accepted methods of analytical research in the field of brewing, biochemistry and proteomics were used to solve the research objectives. The studies allowed us to establish the relationship between the grain and plant-based raw materials used, as well as the processing technologies and biomolecular profiles of beer. The qualitative profile of the distribution of protein compounds as a framework for the formation of a colloidal system and the role of carbohydrate dextrins and phenol compounds are given. This article provides information about the presence of biogenic compounds in the structure of beer that positively affect the functioning of the body. A critical assessment of the influence of some parameters on the completeness of beer taste by biomolecules is given. Conclusion: the conducted analytical studies allowed us to confirm the hypothesis about the nitrogen structure of beer and the relationship of other biomolecules with protein substances, and to identify the main factors affecting the distribution of biomolecules by fractions.

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32

Malmqvist, M. "BIACORE: an affinity biosensor system for characterization of biomolecular interactions." Biochemical Society Transactions 27, no. 2 (February 1, 1999): 335–40. http://dx.doi.org/10.1042/bst0270335.

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33

Choy, J. H., J. M. Oh, M. Park, K. M. Sohn, and J. W. Kim. "Inorganic–Biomolecular Hybrid Nanomaterials as a Genetic Molecular Code System." Advanced Materials 16, no. 14 (July 19, 2004): 1181–84. http://dx.doi.org/10.1002/adma.200400027.

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34

Zhang, Lexiang, Rokshana Parvin, Mingshuo Chen, Dingmeng Hu, Qihui Fan, and Fangfu Ye. "High-throughput microfluidic droplets in biomolecular analytical system: A review." Biosensors and Bioelectronics 228 (May 2023): 115213. http://dx.doi.org/10.1016/j.bios.2023.115213.

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35

Renner, Julie N. "(Invited) Biomolecular Engineering for Electrochemical Applications in Fuel Cells/Electrolyzers and Beyond." ECS Meeting Abstracts MA2022-02, no. 46 (October 9, 2022): 1713. http://dx.doi.org/10.1149/ma2022-02461713mtgabs.

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Control of ionomer thin film structures on metal surfaces is pivotal for efficient performance in electrochemical devices such as fuel cells and electrolyzers. Unfortunately, the assembly of these thin film structures is difficult to control using conventional methods and ideal arrangements remain unknown. Engineered polypeptides have emerged as powerful biomolecular tools in electrode assembly because binding sites and polypeptide structures can be easily modulated by changing the amino acid sequence. However, no studies have been conducted showing polypeptides can be engineered to interact with ionomers, attach them to metal surfaces, and control their arrangement. Our lab has recently developed this technology, using an elastin-like polypeptide to bind to metals, and bind to acidic and basic ionomer via ionic interactions. We use a quartz crystal microbalance with dissipation to provide detailed information about the loading, thickness, and binding behavior of the polypeptide and ionomer layers. We also use atomic force microscopy and grazing-incidence small-angle X-ray scattering to understand the impact of the biomolecules on ionomer phase separation. Finally, we have analyzed the performance (ionic conductivity) of the assembled films using interdigitated electrodes and electrochemical impedance spectroscopy. Through these techniques, we show that 1) our biomolecular system is highly flexible, easily adapting to different materials, 2) the polypeptide sequence can dictate ionomer phase separated structures, and 3) this system can be used to improve the performance of ionomer thin films and gain structure-function understanding. Generally, our results demonstrate that engineered polypeptides are promising tools for ionomer control in electrode engineering for fuel cells/electrolyzers and beyond. Furthermore, this work demonstrates that the creative combination of applied electrochemistry and biomolecular engineering supported and encouraged by leaders in each field can lead to unique research pathways that benefit heath, energy and the environment.

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Lo, Shu-Cheng, En-Hung Lin, Pei-Kuen Wei, and Wan-Shao Tsai. "A compact imaging spectroscopic system for biomolecular detections on plasmonic chips." Analyst 141, no. 21 (2016): 6126–32. http://dx.doi.org/10.1039/c6an01434h.

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In this study, we demonstrate a compact imaging spectroscopic system for high-throughput detection of biomolecular interactions on plasmonic chips, based on a curved grating as the key element of light diffraction and light focusing.

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Chang, Wei, Hongqiao Chen, Guixiang Jiao, Yi Dou, Lin Liu, Cunmin Qu, Jiana Li, and Kun Lu. "Biomolecular Strategies for Vascular Bundle Development to Improve Crop Yield." Biomolecules 12, no. 12 (November 28, 2022): 1772. http://dx.doi.org/10.3390/biom12121772.

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The need to produce crops with higher yields is critical due to a growing global population, depletion of agricultural land, and severe climate change. Compared with the “source” and “sink” transport systems that have been studied a lot, the development and utilization of vascular bundles (conducting vessels in plants) are increasingly important. Due to the complexity of the vascular system, its structure, and its delicate and deep position in the plant body, the current research on model plants remains basic knowledge and has not been repeated for crops and applied to field production. In this review, we aim to summarize the current knowledge regarding biomolecular strategies of vascular bundles in transport systems (source-flow-sink), allocation, helping crop architecture establishment, and influence of the external environment. It is expected to help understand how to use sophisticated and advancing genetic engineering technology to improve the vascular system of crops to increase yield.

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Pandey, Padmaker, Anamika Pandey, Shruti Singh, and Nikhil Kant Shukla. "Self Assembled Monolayers and Carbon Nanotubes: A Significant Tool’s for Modification of Electrode Surface." Sensor Letters 18, no. 9 (September 1, 2020): 669–85. http://dx.doi.org/10.1166/sl.2020.4280.

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A compromising and well-organized model system is needed for investigating the molecular behaviour of biomolecules as many transduction processes and biological recognition occur at biological surfaces. The application of techniques in interfacial surfaces like one molecule thick films has made a feasible and significant tool for modern scientific studies. Self Assembling Monolayers (SAMs) technology is a very useful means for producing monomolecular films of various biological molecules on different substrates. Carbon Nanotubes (CNTs) have length-to-diameter aspect ratio property which provides a large surface-to-volume ratio, making it an intensely capable material for biomolecular attachments. The incorporation of Carbon Nanotubes (CNTs) with biological systems forming functional assemblies has shown an explored area of research. Organo-sulfur mainly alkanethiol (CnH2n+1–SH) molecules get adsorbed onto CNTs. This phenomenon has grabbed a lot of attention because Self Assembling Monolayers (SAMs) of organo-sulfur compound acts as an example system for understanding important chemical, physical or biological processes.

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Blasie, J. Kent, and Peter Timmins. "Neutron Scattering in Structural Biology and Biomolecular Materials." MRS Bulletin 24, no. 12 (December 1999): 40–47. http://dx.doi.org/10.1557/s0883769400053719.

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The substantial power of both elastic and inelastic neutron-scattering techniques for the investigation of the structure and dynamics of biological systems and related biomolecular-based materials—as with soft matter in the previous article by Lindner and Wignall—arises primarily from the essentially isomorphous nature of the substitution of deuterium for selected hydrogen atoms in these systems, coupled with the exquisite sensitivity of neutron scattering to this isotopic substitution. Since these systems are comprised of large macromolecules and supramolecular assemblies thereof, their essential structures and dynamics extend from the atomic scale up to very large length scales of the Order of 101–104 Å. Hence neutron sources and neutron-scattering spectrometers optimized for longer wavelength (or “cold”) thermal neutrons are necessary in order to most effectively address the structure and dynamics at the longer length scales inherent to these Systems.The large majority of previous neutron-scattering experiments on biological systems have been performed with reactor neutron sources. Some of the more significant of these are briefly summarized in the following sections. They may be categorized in terms of the nature of the intermolecular order, both orientational and positional, within the System of interest and either the elastic neutron-scattering technique employed to investigate their time-averaged structures or the inelastic neutron-scattering technique employed to investigate their dynamics.

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Lin, Yi, Ernst Wagner, and Ulrich Lächelt. "Non-viral delivery of the CRISPR/Cas system: DNA versus RNA versus RNP." Biomaterials Science 10, no. 5 (2022): 1166–92. http://dx.doi.org/10.1039/d1bm01658j.

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Chang, Le, Wenfei Li, Naoto Hori, and Shoji Takada. "3P116 The coarse grained GBSA method for simulations of biomolecular system(04. Nucleic acid binding proteins,Poster)." Seibutsu Butsuri 53, supplement1-2 (2013): S231. http://dx.doi.org/10.2142/biophys.53.s231_1.

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Cao, Yujie, Xi Wei, Yuan Lin, and Fei Sun. "Synthesis of bio-inspired viscoelastic molecular networks by metal-induced protein assembly." Molecular Systems Design & Engineering 5, no. 1 (2020): 117–24. http://dx.doi.org/10.1039/c9me00027e.

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Yip, Ping K., Shumaila Hasan, Zhuo-Hao Liu, and Christopher E. G. Uff. "Characterisation of Severe Traumatic Brain Injury Severity from Fresh Cerebral Biopsy of Living Patients: An Immunohistochemical Study." Biomedicines 10, no. 3 (February 22, 2022): 518. http://dx.doi.org/10.3390/biomedicines10030518.

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Traumatic brain injury (TBI) is an extremely complex disease and current systems classifying TBI as mild, moderate, and severe often fail to capture this complexity. Neuroimaging cannot resolve the cellular and molecular changes due to lack of resolution, and post-mortem tissue examination may not adequately represent acute disease. Therefore, we examined the cellular and molecular sequelae of TBI in fresh brain samples and related these to clinical outcomes. Brain biopsies, obtained shortly after injury from 25 living adult patients suffering severe TBI, underwent immunohistochemical analysis. There were no adverse events. Immunostaining revealed various qualitative cellular and biomolecular changes relating to neuronal injury, dendritic injury, neurovascular injury, and neuroinflammation, which we classified into 4 subgroups for each injury type using the newly devised Yip, Hasan and Uff (YHU) grading system. Based on the Glasgow Outcome Scale-Extended, a total YHU grade of ≤8 or ≥11 had a favourable and unfavourable outcome, respectively. Biomolecular changes observed in fresh brain samples enabled classification of this heterogeneous patient population into various injury severity categories based on the cellular and molecular pathophysiology according to the YHU grading system, which correlated with outcome. This is the first study investigating the acute biomolecular response to TBI.

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Hempel, Tim, Mauricio J. del Razo, Christopher T. Lee, Bryn C. Taylor, Rommie E. Amaro, and Frank Noé. "Independent Markov decomposition: Toward modeling kinetics of biomolecular complexes." Proceedings of the National Academy of Sciences 118, no. 31 (July 28, 2021): e2105230118. http://dx.doi.org/10.1073/pnas.2105230118.

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To advance the mission of in silico cell biology, modeling the interactions of large and complex biological systems becomes increasingly relevant. The combination of molecular dynamics (MD) simulations and Markov state models (MSMs) has enabled the construction of simplified models of molecular kinetics on long timescales. Despite its success, this approach is inherently limited by the size of the molecular system. With increasing size of macromolecular complexes, the number of independent or weakly coupled subsystems increases, and the number of global system states increases exponentially, making the sampling of all distinct global states unfeasible. In this work, we present a technique called independent Markov decomposition (IMD) that leverages weak coupling between subsystems to compute a global kinetic model without requiring the sampling of all combinatorial states of subsystems. We give a theoretical basis for IMD and propose an approach for finding and validating such a decomposition. Using empirical few-state MSMs of ion channel models that are well established in electrophysiology, we demonstrate that IMD models can reproduce experimental conductance measurements with a major reduction in sampling compared with a standard MSM approach. We further show how to find the optimal partition of all-atom protein simulations into weakly coupled subunits.

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ROZUM, JORDAN C., and RÉKA ALBERT. "CONTROLLING THE CELL CYCLE RESTRICTION SWITCH ACROSS THE INFORMATION GRADIENT." Advances in Complex Systems 22, no. 07n08 (November 2019): 1950020. http://dx.doi.org/10.1142/s0219525919500206.

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Boolean models represent a drastic simplification of complex biomolecular systems, and yet accurately predict system properties, e.g., effective control strategies. Why is this? Parameter robustness has been highlighted as a general feature of biomolecular systems and may play an important role in the accuracy of Boolean models. We argue here that a useful way to view a system’s controllability properties is through its repertoire of self-sustaining positive circuits (stable motifs). We examine attractor control and self-sustaining circuits within the cell cycle restriction switch, a bistable regulatory circuit that allows or prevents entry into the cell cycle. We explore this system using three models: a previously published Boolean model, a Hill kinetics model that we construct from the Boolean model using the HillCube methodology, and a reaction-based model we construct from the literature. We highlight the robustness of stable motifs across these three levels of modeling detail. We also show how consideration of control-robust regulatory circuits can aid in parameter specification.

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Fernandes, Henrique S., Nuno M. F. S. A. Cerqueira, Sérgio F. Sousa, and André Melo. "A Molecular Mechanics Energy Partitioning Software for Biomolecular Systems." Molecules 27, no. 17 (August 27, 2022): 5524. http://dx.doi.org/10.3390/molecules27175524.

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The partitioning of the molecular mechanics (MM) energy in calculations involving biomolecular systems is important to identify the source of major stabilizing interactions, e.g., in ligand–protein interactions, or to identify residues with considerable contributions in hybrid multiscale calculations, i.e., quantum mechanics/molecular mechanics (QM/MM). Here, we describe Energy Split, a software program to calculate MM energy partitioning considering the AMBER Hamiltonian and parameters. Energy Split includes a graphical interface plugin for VMD to facilitate the selection of atoms and molecules belonging to each part of the system. Energy Split is freely available at or can be easily installed through the VMD Store.

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ARAI, Morio. "BIACORETM, a System for Biomolecular Interaction Analysis Using Surface Plasmon Resonance." Japanese Journal of Thrombosis and Hemostasis 8, no. 5 (1997): 397–405. http://dx.doi.org/10.2491/jjsth.8.397.

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HIRABAYASHI, Miki, Hiroaki KOJIMA, and Kazuhiro OIWA. "Biomolecular Design of an Integrated Software and Hardware System for Cryptography." Transactions of the Society of Instrument and Control Engineers 46, no. 11 (2010): 730–32. http://dx.doi.org/10.9746/sicetr.46.730.

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Arakawa, Takahiro, Tomoya Sameshima, Yukiko Sato, Taro Ueno, Yoshitaka Shirasaki, Takashi Funatsu, and Shuichi Shoji. "Rapid multi-reagents exchange TIRFM microfluidic system for single biomolecular imaging." Sensors and Actuators B: Chemical 128, no. 1 (December 2007): 218–25. http://dx.doi.org/10.1016/j.snb.2007.06.014.

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Imanaka, Hiroyuki, Koki Dare, and Koreyoshi Imamura. "Molecular design of proteinaceous cushion for sensitive biomolecular interaction detection system." New Biotechnology 33 (July 2016): S72. http://dx.doi.org/10.1016/j.nbt.2016.06.966.

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