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Journal of Biological Physics

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https://read.qxmd.com/read/30903354/monitoring-of-lysozyme-thermal-denaturation-by-volumetric-measurements-and-nanodsf-technique-in-the-presence-of-n-butylurea
#1
Joanna Krakowiak, Magdalena Krajewska, Jarosław Wawer
The results of thermal studies of denaturation of hen egg white lysozyme (HEWL) in water and an aqueous solution of N-butylurea (BU) are presented. High-precision densimetric measurements were used to characterize and analyze the changes of the specific volume, v, during temperature elevation. The temperature of the midpoint of protein denaturation was also determined by nanoDSF technique (differential scanning fluorimetry). The densities of lysozyme solutions were measured at temperatures ranging from 298...
March 22, 2019: Journal of Biological Physics
https://read.qxmd.com/read/30895408/global-diffusion-limitations-during-the-initial-phase-of-the-formation-of-a-protein-corona-around-nanoparticles
#2
Vladimir P Zhdanov
Herein, I illustrate analytically how the global diffusion limitations can influence the first phase of the protein-corona formation at nanoparticles under conditions of intravascular injection. In particular, the concentrations of proteins near the boundaries of the injection region are shown to be comparable with those far from the region. In contrast, the concentrations of proteins inside the injection region may be dramatically smaller than those outside, and the ratio of these two concentrations for proteins of different size may be much higher, by a few orders of magnitude, for smaller proteins...
March 20, 2019: Journal of Biological Physics
https://read.qxmd.com/read/30810960/echo-dephasing-and-heat-capacity-from-constrained-and-unconstrained-dynamics-of-triiodothyronine-nuclear-receptor-protein
#3
Tika Ram Lamichhane, Sharma Paudel, Binod Kumar Yadav, Hari Prasad Lamichhane
The objective of this study is to observe the echo feature curves, vibrational dephasing, and heat capacity of a protein-hormone system taking thyroid hormone receptor-beta (THR-β) as an example. Constrained and unconstrained molecular dynamics simulations are performed by implementing the theory of velocity reassignments to probe the phase coherent state in terms of echo pulses. The constrained vibrations are incorporated by adjusting rigid bonds to all hydrogen atoms with an integrator parameter of 2 fs/step in order to reduce the degrees of freedom whereas 1 fs/step is used in the free vibrations of the atomic cluster...
February 27, 2019: Journal of Biological Physics
https://read.qxmd.com/read/30734136/comparative-studies-on-the-interaction-between-biogenic-polyamines-and-bovine-intestinal-alkaline-phosphatases-spectroscopic-and-theoretical-approaches
#4
Pegah Salehian, Behzad Shareghi, Mansoore Hosseini-Koupaei
In this work, the effect of two organic polyamines (spermine and spermidine) on the fluorescence intensity and activity of bovine intestinal alkaline phosphatase (BIALP) are investigated. The interaction of BIALP with spermine and spermidine was studied in a diethanolamine buffer with 0.5 mM magnesium chloride (pH 9.8) and at two temperatures by using the fluorescence quenching method. Furthermore, the activity of enzyme was studied using UV-Vis spectrophotometry in a diethanolamine buffer with 0.5 mM magnesium chloride, at 37 °C, in the absence and presence of different concentrations of each polyamine (0-5 mM)...
February 7, 2019: Journal of Biological Physics
https://read.qxmd.com/read/30721424/size-dependent-inhibition-of-bacterial-growth-by-chemically-engineered-spherical-zno-nanoparticles
#5
Qurat-Ul-Ain Naqvi, Amber Kanwal, S Qaseem, M Naeem, S Rizwan Ali, M Shaffique, M Maqbool
The antibacterial effect of ZnO nanoparticles is tested against Staphylococcus aureus, (a Gram-positive pathogenic bacterium) from a particle-size, concentration, and surface-defects point of view. Activation of antibacterial activity was achieved by standard well diffusion agar and minimum inhibitory concentration procedures. Our results show that smaller-sized particles are more effective inhibitors of bacterial activity when used in a certain optimum concentration. To reveal the underlying mechanism of the observed size and concentration-dependent bacterial activity inhibition, we measured the concentrations of Zn2+ ions released in each suspension by an inductive couple plasma optical emission spectrophotometer...
February 5, 2019: Journal of Biological Physics
https://read.qxmd.com/read/30707386/modeling-the-interplay-between-dna-pk-artemis-and-atm-in-non-homologous-end-joining-repair-in-g1-phase-of-the-cell-cycle
#6
Maryam Rouhani
Modeling a biological process equips us with more comprehensive insight into the process and a more advantageous experimental design. Non-homologous end joining (NHEJ) is a major double-strand break (DSB) repair pathway that occurs throughout the cell cycle. The objective of the current work is to model the fast and slow phases of NHEJ in G1 phase of the cell cycle following exposure to ionizing radiation (IR). The fast phase contains the major components of NHEJ; Ku70/80 complex, DNA-dependent protein kinase catalytic subunit (DNA-PKcs), and XLF/XRCC4/ligase IV complex (XXL)...
February 1, 2019: Journal of Biological Physics
https://read.qxmd.com/read/30680580/dynamics-and-binding-interactions-of-peptide-inhibitors-of-dengue-virus-entry
#7
Diyana Mohd Isa, Sek Peng Chin, Wei Lim Chong, Sharifuddin M Zain, Noorsaadah Abd Rahman, Vannajan Sanghiran Lee
In this study, we investigate the binding interactions of two synthetic antiviral peptides (DET2 and DET4) on type II dengue virus (DENV2) envelope protein domain III. These two antiviral peptides are designed based on the domain III of the DENV2 envelope protein, which has shown significant inhibition activity in previous studies and can be potentially modified further to be active against all dengue strains. Molecular docking was performed using AutoDock Vina and the best-ranked peptide-domain III complex was further explored using molecular dynamics simulations...
January 24, 2019: Journal of Biological Physics
https://read.qxmd.com/read/30612228/anisotropic-aspects-of-solubility-behavior-in-the-demineralization-of-cortical-bone-revealed-by-xrd-analysis
#8
Sergei Danilchenko, Aleksei Kalinkevich, Mykhailo Zhovner, Vladimir Kuznetsov, He Li, Jufang Wang
Dissolution of cortical bone mineral under demineralization in 0.1 M HCl and 0.1 M EDTA solutions is studied by X-ray diffraction (XRD). The bone specimens (in the form of planar oriented pieces) were cut from a diaphysial fragment of a mature mammal bone so that a cross-section surface and a longitudinal section surface could be analyzed individually. This permitted to compare the dissolution behavior of bone apatite of different morphologies: crystals having the c-axis of the hexagonal unit-cell generally parallel to the long axis of the bone (major morphology) and those having the c-axis almost perpendicular to the bone axis (minor morphology)...
January 5, 2019: Journal of Biological Physics
https://read.qxmd.com/read/30280281/limit-to-steady-state-aerobic-power-of-skeletal-muscles
#9
A Paglietti
Like any other kind of cell, muscle cells produce energy by oxidizing the fuel substrate that they absorb together with the needed oxygen from the surroundings. Oxidation occurs entirely within the cell. It means that the reactants and products of reaction must at some time be dissolved in the cell's cytosol. If a cell operates at steady state, its cytosol composition remains constant. Therefore, the cytosol in a muscle that produces work at steady state must contain a constant amount of fuel, oxygen, and product of reaction dissolved in it...
December 2018: Journal of Biological Physics
https://read.qxmd.com/read/30219980/dynamics-of-blood-flow-modeling-of-f%C3%A3-hraeus-and-f%C3%A3-hraeus-lindqvist-effects-using-a-shear-induced-red-blood-cell-migration-model
#10
Rachid Chebbi
Blood flow in micro capillaries of diameter approximately 15-500 μm is accompanied with a lower tube hematocrit level and lower apparent viscosity as the diameter decreases. These effects are termed the Fåhraeus and Fåhraeus-Lindqvist effects, respectively. Both effects are linked to axial accumulation of red blood cells. In the present investigation, we extend previous works using a shear-induced model for the migration of red blood cells and adopt a model for blood viscosity that accounts for the suspending medium viscosity and local hematocrit level...
December 2018: Journal of Biological Physics
https://read.qxmd.com/read/29974373/aqueous-solution-interactions-with-sex-hormone-binding-globulin-and-estradiol-a-theoretical-investigation
#11
A J da Silva, E S Dos Santos
Sex hormone-binding globulin (SHBG) is a binding protein that regulates the availability of steroid hormones in the plasma. Although best known as a steroid carrier, recent studies have associated SHBG in modulating behavioral aspects related to sexual receptivity. Among steroids, estradiol (17β-estradiol, oestradiol or E2), documented as the most active endogenous female hormone, exerts important physiological roles in both reproductive and non-reproductive functions. In this framework, we employed molecular dynamics (MD) and docking techniques for quantifying the interaction energy between a complex aqueous solution, composed by different salts, SHBG and E2...
December 2018: Journal of Biological Physics
https://read.qxmd.com/read/29968194/radiation-shielding-parameters-of-some-antioxidants-using-monte-carlo-method
#12
Huseyin Ozan Tekin, Mesut Karahan, Turker Tekin Erguzel, Tugba Manici, Muhsin Konuk
In this paper, radiation shielding parameters such as mass attenuation coefficients and half value layer (HVL) of some antioxidants are investigated using MCNPX (version 2.4.0). The validation of the generated MCNPX simulation geometry for antioxidant structures is provided by comparing the results with standard WinXcom data for radiation mass attenuation coefficients of antioxidants. Very good agreement between WİNXCOM and MCNPX was obtained. The results from the validated geometry were used to calculate the shielding parameters of different antioxidants...
December 2018: Journal of Biological Physics
https://read.qxmd.com/read/29948555/quantum-like-behavior-without-quantum-physics-ii-a-quantum-like-model-of-neural-network-dynamics
#13
S A Selesnick, Gualtiero Piccinini
In earlier work, we laid out the foundation for explaining the quantum-like behavior of neural systems in the basic kinematic case of clusters of neuron-like units. Here we extend this approach to networks and begin developing a dynamical theory for them. Our approach provides a novel mathematical foundation for neural dynamics and computation which abstracts away from lower-level biophysical details in favor of information-processing features of neural activity. The theory makes predictions concerning such pathologies as schizophrenia, dementias, and epilepsy, for which some evidence has accrued...
December 2018: Journal of Biological Physics
https://read.qxmd.com/read/29946928/study-of-rheological-properties-of-a%C3%A3-ai-berry-pulp-an-analysis-of-its-time-dependent-behavior-and-the-effect-of-temperature
#14
Henrique C B Costa, Fábio O Arouca, Danylo O Silva, Luiz Gustavo M Vieira
The industry of açai-based products has been growing in the last few years. Knowledge about the physical properties of açai pulp, including its rheology, is essential to the optimization of industrial processes. This work presents the rheological behavior of açai berry pulp in relation to the effects of shear rate, temperature, and time of shearing. The entire study was carried out in the temperature range of 10-70 °C. Açai pulp showed a non-Newtonian, pseudoplastic, and time-dependent behavior. Four upward and backward shear rate cycles were evaluated, resulting in complex hysteresis loops, in which thixotropy and anti-thixotropy zones were observed...
December 2018: Journal of Biological Physics
https://read.qxmd.com/read/30392060/mathematical-expression-of-membrane-potential-based-on-ling-s-adsorption-theory-is-approximately-the-same-as-the-goldman-hodgkin-katz-equation
#15
Hirohisa Tamagawa
The Goldman-Hodgkin-Katz equation (GHK equation), one of the most successful achievements of membrane theory in electrophysiology, can precisely predict the membrane potential. Its conceptual foundation lies in the idea that the transmembrane ion transport across the plasma membrane is responsible for the membrane potential generation. However, the potential virtually equivalent to the membrane potential is generated even across the impermeable membrane. In this work, I discus the membrane potential generation mechanism and find that the potential formula based on the long-dismissed Ling's adsorption theory, which attributes the membrane potential generation to the mobile ion adsorption rather than the transmembrane ion transport, is the same as the GHK equation...
November 3, 2018: Journal of Biological Physics
https://read.qxmd.com/read/30377881/impulsive-control-of-a-nonlinear-dynamical-network-and-its-application-to-biological-networks
#16
Min Luo, Jianfeng Jiao, Ruiqi Wang
The control of nonlinear dynamical systems is always a notable problem in science. According to control theory, suitable inputs for a controllable dynamical system are critical. Previous studies have shown some principles to determine control nodes and design control function. In this work, we propose a new control strategy of nonlinear systems by constructing impulsive control functions, i.e., we can realize the transition from an undesired state to a desired one by controlling appropriately chosen nodes in a discrete manner...
October 31, 2018: Journal of Biological Physics
https://read.qxmd.com/read/30367339/expanding-the-flexibility-of-dynamics-simulation-on-different-size-particle-particle-interactions-by-dielectrophoresis
#17
Sheng Hu, Rongrong Fu
In this paper, we perform flexible and reliable dynamics simulations on different sizes of two or more particles' interactive motions, where they encounter positive or negative dielectrophoresis (DEP) forces. The particles with identical or non-identical size are in close proximity suspended freely in a solution under a homogeneous electric field. According to the description of classic dipole moment, DEP forces make the particles form a straight chain. Therefore, dynamics simulation based on Newton's laws is utilized to understand AC DEP phenomena among multiple particles...
October 26, 2018: Journal of Biological Physics
https://read.qxmd.com/read/30361812/physiological-and-biochemical-responses-of-makhana-euryale-ferox-to-gamma-irradiation
#18
Nitish Kumar, Shweta Rani, Gaurav Kuamr, Swati Kumari, Indu Shekhar Singh, S Gautam, Binod Kumar Choudhary
The impact of gamma irradiation on growth and physiology of Euryale ferox was described in the present investigation. E. ferox is an underutilized aquatic food crop that grows in shallow-water bodies in lower Assam regions and north Bihar of India. The seeds of E. ferox were irradiated with different doses of gamma irradiation ranging from 0 to 500 Gy. It was observed that the germination and survival percentage was inhibited by increasing the irradiation dose. However, plants developed from seed exposed to an irradiation dose beyond 100 Gy did not survive more than 1 month...
October 25, 2018: Journal of Biological Physics
https://read.qxmd.com/read/30209704/modeling-of-a-single-nanoparticle-interaction-with-the-human-blood-plasma-proteins
#19
Vladas Skakauskas, Pranas Katauskis
When nanoparticles are introduced into a physiological environment, proteins and lipids immediately cover their surface, forming a protein "corona". It is well recognized that the corona structure influences the biological response of the body. Two deterministic models for corona formation of the human blood serum proteins around a single nanoparticle are presented and studied numerically in this paper. One of them is based on a coupled system of PDEs and involves diffusion of proteins toward the nanoparticle surface...
September 12, 2018: Journal of Biological Physics
https://read.qxmd.com/read/29971755/charge-transport-in-a-dna-model-with-solvent-interaction
#20
H Ngoubi, G H Ben-Bolie, T C Kofané
The charge transport in the modified DNA model is studied by taking into account the factor of solvent and the effect of coupling motions of nucleotides. We report on the presence of the modulational instability (MI) of a plane wave for charge migration in DNA and the generation of soliton-like excitations in DNA nucleotides. By applying the continuum approximation, we show that the original differential-difference equation for the DNA dynamics can be reduced to a set of three coupled nonlinear equations. The linear stability analysis of wave solutions of the coupled systems is performed and the growth rate of instability is found numerically...
September 2018: Journal of Biological Physics
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