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Journal of Biological Physics

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https://www.readbyqxmd.com/read/29974373/aqueous-solution-interactions-with-sex-hormone-binding-globulin-and-estradiol-a-theoretical-investigation
#1
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...
July 5, 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29971755/charge-transport-in-a-dna-model-with-solvent-interaction
#2
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...
July 3, 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29968194/radiation-shielding-parameters-of-some-antioxidants-using-monte-carlo-method
#3
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...
July 2, 2018: Journal of Biological Physics
https://www.readbyqxmd.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
#4
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...
June 26, 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29948555/quantum-like-behavior-without-quantum-physics-ii-a-quantum-like-model-of-neural-network-dynamics
#5
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...
June 8, 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29882183/changes-of-cationic-transport-in-atcax5-transformant-yeast-by-electromagnetic-field-environments
#6
Munmyong Choe, Won Choe, Songchol Cha, Imshik Lee
The electromagnetic field (EMF) is newly considered as an exogenous environmental stimulus that is closely related to ion transportation on the cellular membrane, maintaining the internal ionic homeostasis. Cation transports of Ca2+ and other metal ions, Cd2+ , Zn2+ , and Mn2+ were studied in terms of the external Ca2+ stress, [Ca2+ ]ext , and exposure to the physical EMF. A specific yeast strain K667 was used for controlling CAX5 (cation/H+ exchanger) expression. Culture samples were exposed to 60 Hz, 0.1 mT sinusoidal or square magnetics waves, and intracellular cations of each sample were measured and analyzed...
June 7, 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29860641/fitting-of-dynamic-recurrent-neural-network-models-to-sensory-stimulus-response-data
#7
R Ozgur Doruk, Kechen Zhang
We present a theoretical study aiming at model fitting for sensory neurons. Conventional neural network training approaches are not applicable to this problem due to lack of continuous data. Although the stimulus can be considered as a smooth time-dependent variable, the associated response will be a set of neural spike timings (roughly the instants of successive action potential peaks) that have no amplitude information. A recurrent neural network model can be fitted to such a stimulus-response data pair by using the maximum likelihood estimation method where the likelihood function is derived from Poisson statistics of neural spiking...
June 2, 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29850983/mn-2-concentrations-in-coastal-fish-otoliths-understanding-environmental-and-biological-influences-from-epr
#8
Ana Paula Madeira Di Beneditto, Roberto Weider de Assis Franco
The Mn2+ concentrations in the sagittae otoliths of 12 fish families (and 19 species) that co-occur in a coastal area of southeastern Brazil (~21°S) were quantified using electron paramagnetic resonance (EPR). Inferences were made about the relationship between fish habitat and trace element incorporation. Inferences were made on the relationship between trace element concentration and otolith shape. The differences in Mn2+ concentrations among the species suggest that habitat (and feeding habits) might drive the incorporation of this trace element into fish otoliths, with higher values in bottom-associated fish species than in surface-associated species...
May 30, 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29808371/in-vivo-mimicking-model-for-solid-tumor-towards-hydromechanics-of-tissue-deformation-and-creation-of-necrosis
#9
Bibaswan Dey, G P Raja Sekhar, Sourav Kanti Mukhopadhyay
The present work addresses transvascular and interstitial fluid transport inside a solid tumor surrounded by normal tissue (close to an in vivo mimicking setup). In general, biological tissues behave like a soft porous material and show mechanical behavior towards the fluid motion through the interstitial space. In general, forces like viscous drag that are associated with the fluid flow may compress the tissue material. On the macroscopic level, we try to model the motion of fluids and macromolecules through the interstitial space of solid tumor and the normal tissue layer...
May 28, 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29796745/is-a-constant-low-entropy-process-at-the-root-of-glycolytic-oscillations
#10
Henrik Seir Thoke, Lars F Olsen, Lars Duelund, R P Stock, Thomas Heimburg, Luis A Bagatolli
We measured temporal oscillations in thermodynamic variables such as temperature, heat flux, and cellular volume in suspensions of non-dividing yeast cells which exhibit temporal glycolytic oscillations. Oscillations in these variables have the same frequency as oscillations in the activity of intracellular metabolites, suggesting strong coupling between them. These results can be interpreted in light of a recently proposed theoretical formalism in which isentropic thermodynamic systems can display coupled oscillations in all extensive and intensive variables, reminiscent of adiabatic waves...
May 24, 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29752596/laser-interferometry-of-the-hydrolytic-changes-in-protein-solutions-the-refractive-index-and-hydration-shells
#11
R M Sarimov, T A Matveyeva, V N Binhi
Using an original laser interferometer of enhanced sensitivity, an increase in the refractive index of a protein solution was observed during the reaction of proteolysis catalyzed by pepsin. The increase in the refractive index of the protein solution at a concentration of 4 mg/ml was [Formula: see text] for bovine serum albumin and [Formula: see text] for lysozyme. The observed effect disproves the existing idea that the refractive index of protein solutions is determined only by their amino acid composition and concentration...
May 11, 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29740739/fe-ii-formation-after-interaction-of-the-amyloid-%C3%AE-peptide-with-iron-storage-protein-ferritin
#12
Lucia Balejcikova, Katarina Siposova, Peter Kopcansky, Ivo Safarik
The interaction of amyloid β-peptide (Aβ) with the iron-storage protein ferritin was studied in vitro. We have shown that Aβ during fibril formation process is able to reduce Fe(III) from the ferritin core (ferrihydrite) to Fe(II). The Aβ-mediated Fe(III) reduction yielded a two-times-higher concentration of free Fe(II) than the spontaneous formation of Fe(II) by the ferritin itself. We suggest that Aβ can also act as a ferritin-specific metallochaperone-like molecule capturing Fe(III) from the ferritin ferrihydrite core...
May 9, 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29732506/terahertz-infrared-spectroscopy-of-shewanella-oneidensis-mr-1-extracellular-matrix
#13
Z V Gagkaeva, E S Zhukova, V Grinenko, A K Grebenko, K V Sidoruk, T A Voeikova, M Dressel, B P Gorshunov
Employing optical spectroscopy we have performed a comparative study of the dielectric response of extracellular matrix and filaments of electrogenic bacteria Shewanella oneidensis MR-1, cytochrome c, and bovine serum albumin. Combining infrared transmission measurements on thin layers with data of the terahertz spectra, we obtain the dielectric permittivity and AC conductivity spectra of the materials in a broad frequency band from a few cm-1 up to 7000 cm-1 in the temperature range from 5 to 300 K. Strong absorption bands are observed in the three materials that cover the range from 10 to 300 cm-1 and mainly determine the terahertz absorption...
May 7, 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29671097/foreword
#14
EDITORIAL
Roya Zandi, Cristian Micheletti, Rudolf Podgornik
No abstract text is available yet for this article.
June 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29656365/characterization-of-aav-vector-particle-stability-at-the-single-capsid-level
#15
Julien Bernaud, Axel Rossi, Anny Fis, Lara Gardette, Ludovic Aillot, Hildegard Büning, Martin Castelnovo, Anna Salvetti, Cendrine Faivre-Moskalenko
Virus families have evolved different strategies for genome uncoating, which are also followed by recombinant vectors. Vectors derived from adeno-associated viruses (AAV) are considered as leading delivery tools for in vivo gene transfer, and in particular gene therapy. Using a combination of atomic force microscopy (AFM), biochemical experiments, and physical modeling, we investigated here the physical properties and stability of AAV vector particles. We first compared the morphological properties of AAV vectors derived from two different serotypes (AAV8 and AAV9)...
June 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29654426/direct-visualization-of-single-virus-restoration-after-damage-in-real-time
#16
Pedro J de Pablo, Mercedes Hernando-Pérez, Carolina Carrasco, José L Carrascosa
We use the nano-dissection capabilities of atomic force microscopy to induce structural alterations on individual virus capsids in liquid milieu. We fracture the protein shells either with single nanoindentations or by increasing the tip-sample interaction force in amplitude modulation dynamic mode. The normal behavior is that these cracks persist in time. However, in very rare occasions they self-recuperate to retrieve apparently unaltered virus particles. In this work, we show the topographical evolution of three of these exceptional events occurring in T7 bacteriophage capsids...
June 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29644513/folding-a-viral-peptide-in-different-membrane-environments-pathway-and-sampling-analyses
#17
Shivangi Nangia, Jason G Pattis, Eric R May
Flock House virus (FHV) is a well-characterized model system to study infection mechanisms in non-enveloped viruses. A key stage of the infection cycle is the disruption of the endosomal membrane by a component of the FHV capsid, the membrane active γ peptide. In this study, we perform all-atom molecular dynamics simulations of the 21 N-terminal residues of the γ peptide interacting with membranes of differing compositions. We carry out umbrella sampling calculations to study the folding of the peptide to a helical state in homogenous and heterogeneous membranes consisting of neutral and anionic lipids...
June 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29637472/curating-viscoelastic-properties-of-icosahedral-viruses-virus-based-nanomaterials-and-protein-cages
#18
Ravi Kant, Vamseedhar Rayaprolu, Kaitlyn McDonald, Brian Bothner
The beauty, symmetry, and functionality of icosahedral virus capsids has attracted the attention of biologists, physicists, and mathematicians ever since they were first observed. Viruses and protein cages assemble into functional architectures in a range of sizes, shapes, and symmetries. To fulfill their biological roles, these structures must self-assemble, resist stress, and are often dynamic. The increasing use of icosahedral capsids and cages in materials science has driven the need to quantify them in terms of structural properties such as rigidity, stiffness, and viscoelasticity...
June 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29616429/the-different-faces-of-mass-action-in-virus-assembly
#19
Bart van der Holst, Willem K Kegel, Roya Zandi, Paul van der Schoot
The spontaneous encapsulation of genomic and non-genomic polyanions by coat proteins of simple icosahedral viruses is driven, in the first instance, by electrostatic interactions with polycationic RNA binding domains on these proteins. The efficiency with which the polyanions can be encapsulated in vitro, and presumably also in vivo, must in addition be governed by the loss of translational and mixing entropy associated with co-assembly, at least if this co-assembly constitutes a reversible process. These forms of entropy counteract the impact of attractive interactions between the constituents and hence they counteract complexation...
June 2018: Journal of Biological Physics
https://www.readbyqxmd.com/read/29607454/molecular-dynamics-study-of-t-3-capsid-assembly
#20
D C Rapaport
Molecular dynamics simulation is used to model the self-assembly of polyhedral shells containing 180 trapezoidal particles that correspond to the T = 3 virus capsid. Three kinds of particle, differing only slightly in shape, are used to account for the effect of quasi-equivalence. Bond formation between particles is reversible and an explicit atomistic solvent is included. Under suitable conditions the simulations are able to produce complete shells, with the majority of unused particles remaining as monomers, and practically no other clusters...
June 2018: Journal of Biological Physics
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