scholarly journals Transcription-Based Amplified Colorimetric Thrombin Sensor Using Non-Crosslinking Aggregation of DNA-Modified Gold Nanoparticles

Sensors ◽  
2021 ◽  
Vol 21 (13) ◽  
pp. 4318
Author(s):  
Yu Muto ◽  
Gen Hirao ◽  
Tamotsu Zako
Keyword(s):  
Gold Nanoparticles ◽  
Conformational Change ◽  
Structural Changes ◽  
Detection System ◽  
Color Difference ◽  
Measurement Sensitivity ◽  
Improve Measurement ◽  
Wide Range ◽  
Duplex Formation ◽  
Rna Promoter

Gold nanoparticles (AuNPs) have been employed as colorimetric biosensors due to the color difference between their dispersed (red) and aggregated (blue) states. Although signal amplification reactions triggered by structural changes of the ligands on AuNPs have been widely used to improve measurement sensitivity, the use of ligands is limited. In this study, we designed a AuNP-based signal-amplifying sandwich biosensor, which does not require a conformational change in the ligands. Thrombin was used as a model target, which is recognized by two different probes. In the presence of the target, an extension reaction occurs as a result of hybridization of the two probes. Then RNA synthesis is started by RNA polymerase activation due to RNA promoter duplex formation. The amplified RNA drives aggregation or dispersion of the AuNPs, and a difference of the color if the AuNP solution is observed. As this detection system does not require a conformational change in the ligand, it can be generically applied to a wide range ligands.

scholarly journals Entangling Lattice-Trapped Bosons with a Free Impurity: Impact on Stationary and Dynamical Properties

Entropy ◽  
2021 ◽  
Vol 23 (3) ◽  
pp. 290
Author(s):  
Maxim Pyzh ◽  
Kevin Keiler ◽  
Simeon I. Mistakidis ◽  
Peter Schmelcher
Keyword(s):  
Structural Changes ◽  
Many Body ◽  
Wide Range ◽  
Entropy Measures ◽  
Particle Level ◽  
The Many ◽  
The One ◽  
Tunneling Dynamics ◽  
The Individual ◽  
Trapped Bosons

We address the interplay of few lattice trapped bosons interacting with an impurity atom in a box potential. For the ground state, a classification is performed based on the fidelity allowing to quantify the susceptibility of the composite system to structural changes due to the intercomponent coupling. We analyze the overall response at the many-body level and contrast it to the single-particle level. By inspecting different entropy measures we capture the degree of entanglement and intraspecies correlations for a wide range of intra- and intercomponent interactions and lattice depths. We also spatially resolve the imprint of the entanglement on the one- and two-body density distributions showcasing that it accelerates the phase separation process or acts against spatial localization for repulsive and attractive intercomponent interactions, respectively. The many-body effects on the tunneling dynamics of the individual components, resulting from their counterflow, are also discussed. The tunneling period of the impurity is very sensitive to the value of the impurity-medium coupling due to its effective dressing by the few-body medium. Our work provides implications for engineering localized structures in correlated impurity settings using species selective optical potentials.

scholarly journals Ligand-induced structural changes analysis of ribose-binding protein as studied by molecular dynamics simulations

2021 ◽  
pp. 1-12
Author(s):  
Haiyan Li ◽  
Zanxia Cao ◽  
Guodong Hu ◽  
Liling Zhao ◽  
Chunling Wang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Changes ◽  
Binding Protein ◽  
Network Models ◽  
Md Simulations ◽  
Protein Domain ◽  
Opening Angle ◽  
Conformation Changes ◽  
Wide Range ◽  
Ribose Binding Protein

BACKGROUND: The ribose-binding protein (RBP) from Escherichia coli is one of the representative structures of periplasmic binding proteins. Binding of ribose at the cleft between two domains causes a conformational change corresponding to a closure of two domains around the ligand. The RBP has been crystallized in the open and closed conformations. OBJECTIVE: With the complex trajectory as a control, our goal was to study the conformation changes induced by the detachment of the ligand, and the results have been revealed from two computational tools, MD simulations and elastic network models. METHODS: Molecular dynamics (MD) simulations were performed to study the conformation changes of RBP starting from the open-apo, closed-holo and closed-apo conformations. RESULTS: The evolution of the domain opening angle θ clearly indicates large structural changes. The simulations indicate that the closed states in the absence of ribose are inclined to transition to the open states and that ribose-free RBP exists in a wide range of conformations. The first three dominant principal motions derived from the closed-apo trajectories, consisting of rotating, bending and twisting motions, account for the major rearrangement of the domains from the closed to the open conformation. CONCLUSIONS: The motions showed a strong one-to-one correspondence with the slowest modes from our previous study of RBP with the anisotropic network model (ANM). The results obtained for RBP contribute to the generalization of robustness for protein domain motion studies using either the ANM or PCA for trajectories obtained from MD.

scholarly journals Design of a Microwave Power Detection System in the 5G-Communication Frequency Band

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2674
Author(s):  
Qingying Ren ◽  
Wen Zuo ◽  
Jie Xu ◽  
Leisheng Jin ◽  
Wei Li ◽  
...  
Keyword(s):  
Frequency Band ◽  
Microwave Power ◽  
Communication Systems ◽  
Detection System ◽  
Measurement Sensitivity ◽  
Detection Range ◽  
Detection Systems ◽  
Detection Frequency ◽  
Communication Frequency ◽  
5G Communication

At present, the proposed microwave power detection systems cannot provide a high dynamic detection range and measurement sensitivity at the same time. Additionally, the frequency band of these detection systems cannot cover the 5G-communication frequency band. In this work, a novel microwave power detection system is proposed to measure the power of the 5G-communication frequency band. The detection system is composed of a signal receiving module, a power detection module and a data processing module. Experiments show that the detection frequency band of this system ranges from 1.4 GHz to 5.3 GHz, the dynamic measurement range is 70 dB, the minimum detection power is −68 dBm, and the sensitivity is 22.3 mV/dBm. Compared with other detection systems, the performance of this detection system in the 5G-communication frequency band is significantly improved. Therefore, this microwave power detection system has certain reference significance and application value in the microwave signal detection of 5G communication systems.

scholarly journals Overview of Popular Techniques of Raman Spectroscopy and Their Potential in the Study of Plant Tissues

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1537
Author(s):  
Aneta Saletnik ◽  
Bogdan Saletnik ◽  
Czesław Puchalski
Keyword(s):  
Raman Spectroscopy ◽  
Cell Walls ◽  
Structural Changes ◽  
Spatial Information ◽  
Technological Development ◽  
Analytical Techniques ◽  
High Sensitivity ◽  
Plant Tissues ◽  
Wide Range ◽  
Identification Technique

Raman spectroscopy is one of the main analytical techniques used in optical metrology. It is a vibration, marker-free technique that provides insight into the structure and composition of tissues and cells at the molecular level. Raman spectroscopy is an outstanding material identification technique. It provides spatial information of vibrations from complex biological samples which renders it a very accurate tool for the analysis of highly complex plant tissues. Raman spectra can be used as a fingerprint tool for a very wide range of compounds. Raman spectroscopy enables all the polymers that build the cell walls of plants to be tracked simultaneously; it facilitates the analysis of both the molecular composition and the molecular structure of cell walls. Due to its high sensitivity to even minute structural changes, this method is used for comparative tests. The introduction of new and improved Raman techniques by scientists as well as the constant technological development of the apparatus has resulted in an increased importance of Raman spectroscopy in the discovery and defining of tissues and the processes taking place in them.

scholarly journals Combining experimental and simulation data of molecular processes via augmented Markov models

2017 ◽  
Vol 114 (31) ◽  
pp. 8265-8270 ◽  
Author(s):  
Simon Olsson ◽  
Hao Wu ◽  
Fabian Paul ◽  
Cecilia Clementi ◽  
Frank Noé
Keyword(s):  
Force Field ◽  
Structural Changes ◽  
Markov Models ◽  
Force Fields ◽  
Divide And Conquer ◽  
Simulation Data ◽  
Wide Range ◽  
Simulation And Experiment ◽  
Kinetics Of

Accurate mechanistic description of structural changes in biomolecules is an increasingly important topic in structural and chemical biology. Markov models have emerged as a powerful way to approximate the molecular kinetics of large biomolecules while keeping full structural resolution in a divide-and-conquer fashion. However, the accuracy of these models is limited by that of the force fields used to generate the underlying molecular dynamics (MD) simulation data. Whereas the quality of classical MD force fields has improved significantly in recent years, remaining errors in the Boltzmann weights are still on the order of a few kT, which may lead to significant discrepancies when comparing to experimentally measured rates or state populations. Here we take the view that simulations using a sufficiently good force-field sample conformations that are valid but have inaccurate weights, yet these weights may be made accurate by incorporating experimental data a posteriori. To do so, we propose augmented Markov models (AMMs), an approach that combines concepts from probability theory and information theory to consistently treat systematic force-field error and statistical errors in simulation and experiment. Our results demonstrate that AMMs can reconcile conflicting results for protein mechanisms obtained by different force fields and correct for a wide range of stationary and dynamical observables even when only equilibrium measurements are incorporated into the estimation process. This approach constitutes a unique avenue to combine experiment and computation into integrative models of biomolecular structure and dynamics.

Study of Properties of Expanded Graphite – Polymer Porous Composite by Acoustic Emission Method

2013 ◽  
Vol 58 (4) ◽  
pp. 1331-1336 ◽  
Author(s):  
J. Berdowski ◽  
S. Berdowska ◽  
F. Aubry
Keyword(s):  
Acoustic Emission ◽  
Structural Changes ◽  
Structural Characteristics ◽  
Physical And Mechanical Properties ◽  
Expanded Graphite ◽  
Composite Membranes ◽  
Acoustic Emission Method ◽  
Emission Method ◽  
Graphite Composite ◽  
Wide Range

Abstract The purpose of this paper was to investigate the physical and mechanical properties of compressed expanded graphite (CEG) and their porous derivatives after impregnation, polymerization; and carbonization by the use of acoustic emission method (AE). The mechanical and structural characteristics of compressed expanded graphite and their three groups of porous composites after each technological process are presented and discussed. The measurements of acoustic emission parameters in these materials were carried out at wide range of frequency of the waves (0.1÷2.5 MHz). The changes of two of parameters: - AE pulses counts rate and spectrum distribution of AE waves - are presented in this paper. The analysis of the respective parameters AE also gives possibility to determine the micro- and macro structural changes of materials at different levels of technological processes. Applications of these materials as catalysts with high specific surface make them very interesting subject of study. Also compressed expanded graphite composite membranes prepared from furfuryl alcohol polymers are promising for gas separation.

SHELL DEFORMATION AND SPIN EFFECTS IN NUCLEON SEPARATION ENERGIES

1993 ◽  
Vol 02 (04) ◽  
pp. 789-807
Author(s):  
D. CALEB CHANTHI RAJ ◽  
M. RAJASEKARAN ◽  
R. PREMANAND
Keyword(s):  
Structural Changes ◽  
Shell Correction ◽  
Separation Energy ◽  
Systematic Analysis ◽  
Spin Effects ◽  
Wide Range ◽  
Type Calculation ◽  
Nucleon Separation Energy ◽  
New Formula ◽  
Good Agreement

A new formula to obtain shell correction to separation energy is derived from a Strutinsky type calculation. A systematic analysis of shell and deformation effects on nucleon separation energy is made. Spin induced structural changes are also evident in shape changes along the spin coordinate. Calculations are performed for a wide range of nuclei from Zr to Cm. The results are generally in very good agreement with experimental analysis.

scholarly journals COMPARATIVE ANALYSIS OF DIFFERENT CRITERIA OF SITE STRUCTURAL STABILITY IN THE TIME SERIES

2019 ◽  
pp. 119-128
Author(s):  
Liliya Andreevna Landman ◽  
Andrei Vladimirovich Faddeenkov
Keyword(s):  
Time Series ◽  
Regression Model ◽  
Structural Changes ◽  
Least Squares Method ◽  
Complex Structure ◽  
Standard Normal Distribution ◽  
Regression Equations ◽  
Unknown Parameters ◽  
Chow Test ◽  
Wide Range

The concept of structure is used to describe a set of stable relations between the main parts of the object, which describe its integrity and identity, i.e, preserving the basic properties for a wide range of internal and external changes. This concept usually relates to the concepts of system and organization. The structure expresses a stable part of the system that is slightly changed during different reforms. Over the years structural changes take place because of active economic policy or as a result of spontaneous, uncontrollable processes. Therefore, it seems to be quite natural to find out whether there have been structural changes in the observation period, and to find them reflected in the specification of the model. The basic ideas of methods for determining structural changes in the time series dynamics have been considered, such as Chow test, Gujarati test and Poirier method. The power study was conducted for the three possible cases of change in time series trends. The random error was modeled according to the standard normal distribution. A linear multiple regression model with three independent variables was used as a time series model. Estimation of the vector of unknown parameters of the model was conducted using least squares method. For each of the three criteria the of test the null hypothesis about time series instability was carried out using the F -criterion, which involves finding the residual sum of squares of a regression model and analysis of correlation between its decline and the loss of degrees of freedom. It can be noted that Gujarati and Poirier equations have a more complex structure than equation of Chow test; however, using Chow test assumes estimation of the parameters of the three regression equations.

scholarly journals Size matters: Size Dependency of Gold Nanoparticles Interacting with Model Membranes

2019 ◽  
Author(s):  
Claudia Contini ◽  
James W. Hindley ◽  
Tom Macdonald ◽  
Joseph Barritt ◽  
Oscar Ces ◽  
...  
Keyword(s):  
Gold Nanoparticles ◽  
Lipid Bilayers ◽  
Lipid Membrane ◽  
Rapid Development ◽  
Membrane System ◽  
Size Dependent ◽  
Research Fields ◽  
Large Unilamellar Vesicles ◽  
Wide Range ◽  
Experimental Characterisation

<p><b>The rapid development of nanomaterials has led to an increase in the number and variety of engineered nanomaterials (ENMs) in the environment. Gold nanoparticles (AuNPs) are an example of a commonly studied ENM whose highly tailorable properties have generated significant interest through a wide range of research fields. In the present work, we report the first qualitative as well as quantitative experimental characterisation of the AuNP-membrane interaction. We investigate the interactions between citrate-stabilised AuNPs (diameters 5, 10, 25, 35, 50, 60 nm) and large unilamellar vesicles (LUVs) acting as a model membrane system. LUVs were prepared in two different formulations using 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) and 1,2-dileoyl-sn-glycero-3-phosphocholine (DOPC). Our results show that the interaction between AuNPs and LUVs is size dependent; in particular, we reveal the existence of two AuNP’s critical diameters which determine the fate of AuNPs in contact with a lipid membrane. The results provide a new understanding of the size dependent interaction between AuNPs and lipid bilayers of direct relevance to nanotoxicology and to the design of NP vectors.</b></p>

scholarly journals Simultaneous Monitoring of Crystalline Active Materials and Resistance Evolution in Lithium-Sulfur Batteries

2019 ◽  
Author(s):  
Yu-Chuan Chien ◽  
Ashok Menon ◽  
William Brant ◽  
Daniel Brandell ◽  
Matthew Lacey
Keyword(s):  
Energy Storage ◽  
Structural Changes ◽  
Dissolution Kinetics ◽  
Carbon Composite ◽  
Diffusion Resistance ◽  
Active Materials ◽  
Host Matrix ◽  
Current Interruption ◽  
Wide Range ◽  
Lithium Sulfur

Operando X-ray diffraction (XRD) is a valuable tool for studying secondary battery materials as it allows for the direct correlation of electrochemical behavior with structural changes of crystalline active materials. This is especially true for the lithium-sulfur chemistry, in which energy storage capability depends on the complex growth and dissolution kinetics of lithium sulfide (Li2S) and sulfur (S8) during discharge and charge, respectively. In this work, we present a novel development of this method through combining operando XRD with simultaneous and continuous resistance measurement using an Intermittent Current Interruption (ICI) method. We show that a coefficient of diffusion resistance, which reflects the transport properties in the sulfur/carbon composite electrode, can be determined from analysis of each current interruption. Its relationship to the established Warburg impedance model is validated theoretically and experimentally. We also demonstrate for an optimized electrode formulation and cell construction that the diffusion resistance increases sharply at the discharge end point, which is consistent with the blocking of pores in the carbon host matrix. The combination of XRD with ICI allows for a direct correlation of structural changes with not only electrochemical properties but also energy loss processes at a non-equilibrium state, and therefore is a valuable technique for the study of a wide range of energy storage chemistries.<br>

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