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Journal of Biological Physics

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
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
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
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
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
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
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
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
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
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
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
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
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
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...
September 2018: Journal of Biological Physics
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...
September 2018: Journal of Biological Physics
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...
September 2018: Journal of Biological Physics
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...
September 2018: Journal of Biological Physics
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...
September 2018: Journal of Biological Physics
Klaus Jaffe
Computer experiments that mirror the evolutionary dynamics of sexual and asexual organisms as they occur in nature were used to test features proposed to explain the evolution of sexual recombination. Results show that this evolution is better described as a network of interactions between possible sexual forms, including diploidy, thelytoky, facultative sex, assortation, bisexuality, and division of labor between the sexes, rather than a simple transition from parthenogenesis to sexual recombination. Diploidy was shown to be fundamental for the evolution of sex; bisexual reproduction emerged only among anisogamic diploids with a synergistic division of reproductive labor; and facultative sex was more likely to evolve among haploids practicing assortative mating...
September 2018: Journal of Biological Physics
Guo-Hua Li
The P2X receptor is a trimeric transmembrane protein that acts as an ATP-gated ion channel. Its transmembrane domain (TMD) contains only six helices and three of them, the M2 helices, line the ion conduction pathway. Here, using molecular dynamics simulation, I identify four conformational states of the TMD that are associated with four types of packing between M2 helices. Packing in the extracellular half of the M2 helix produces closed conformations, while packing in the intracellular half produces both open and closed conformations...
September 2018: Journal of Biological Physics
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