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Journal of Biological Physics

Ziad Khattari
The secondary structure of apolipoprotein B-100 is studied within the bulk phase and at the air/water interface. In these "in viro" experiments, infrared reflection absorption spectroscopy (IRRAS) study was performed at the air/water interface while circular dichroism (CD) was conducted in the bulk phase. In the bulk phase, the conformational structure containing a significant amount of β-structure, whereas varying amount of α-helix, unordered structures, and β-sheet were observed at the air/water interface depending on the low-density lipoprotein (LDL) film interfacial pressure...
June 24, 2017: Journal of Biological Physics
A Halmagyi, E Surducan, V Surducan
Two distinct microwave power levels and techniques have been studied in two cases: low-power microwave (LPM) irradiation on in vitro Sequoia plants and high-power microwave (HPM) exposure on recovery rates of cryostored (-196°C) Sequoia shoot apices. Experimental variants for LPM exposure included: (a) in vitro plants grown in regular conditions (at 24 ± 1°C during a 16-h light photoperiod with a light intensity of 39.06 μEm(-2) s(-1) photosynthetically active radiation), (b) in vitro plants grown in the anechoic chamber with controlled environment without microwave irradiation, and (c) in vitro plants grown in the anechoic chamber with LPM irradiation for various times (5, 15, 30, 40 days)...
June 24, 2017: Journal of Biological Physics
Hirohisa Tamagawa, Kota Ikeda
Donnan theory and Goldman-Hodgkin-Katz equation (GHK eq.) state that the nonzero membrane potential is generated by the asymmetric ion distribution between two solutions separated by a semipermeable membrane and/or by the continuous ion transport across the semipermeable membrane. However, there have been a number of reports of the membrane potential generation behaviors in conflict with those theories. The authors of this paper performed the experimental and theoretical investigation of membrane potential and found that (1) Donnan theory is valid only when the macroscopic electroneutrality is sufficed and (2) Potential behavior across a certain type of membrane appears to be inexplicable on the concept of GHK eq...
May 30, 2017: Journal of Biological Physics
Konda Mani Saravanan, Samuel Selvaraj
In theory, a polypeptide chain can adopt a vast number of conformations, each corresponding to a set of backbone rotation angles. Many of these conformations are excluded due to steric overlaps. Ramachandran and coworkers were the first to look into this problem by plotting backbone dihedral angles in a two-dimensional plot. The conformational space in the Ramachandran map is further refined by considering the energetic contributions of various non-bonded interactions. Alternatively, the conformation adopted by a polypeptide chain may also be examined by investigating interactions between the residues...
June 2017: Journal of Biological Physics
Aldo Ledesma-Durán, Lorenzo-Héctor Juárez-Valencia, Juan-Bibiano Morales-Malacara, Iván Santamaría-Holek
Every morphological, behavioral, or even developmental character expression of living beings is coded in its genotype and is expressed in its phenotype. Nevertheless, the interplay between phenotypic and ontogenetic plasticities, that is, the capability to manifest trait variations, is a current field of research that needs morphometric, numerical, or even mathematical modeling investigations. In the present work, we are searching for a phenotypic index able to identify the underlying correlation among phenotypic, ontogenetic, and geographic distribution of the evolutionary development of species of the same genus...
June 2017: Journal of Biological Physics
Oleksandr Barannyk, Robert Fraser, Peter Oshkai
In this paper, a long-term in vitro dynamic calcification of three porcine aortic heart valves was investigated using a combined approach that involved accelerated wear testing of the valves in the rapid calcification solution, hydrodynamic assessment of the progressive change of effective orifice area (EOA) along with the transaortic pressure gradient, and quantitative visualization of the flow. The motivation for this study was developing a standardized, economical, and feasible in vitro testing methodology for bioprosthetic heart valve calcification, which would address both the hydrodynamic performance of the valves as well as the subsequent changes in the flow field...
June 2017: Journal of Biological Physics
P K Tiwari, A K Misra, Ezio Venturino
Synthetic fertilizers and livestock manure are nowadays widely used in agriculture to improve crop yield but nitrogen and phosphorous runoff resulting from their use compromises water quality and contributes to eutrophication phenomena in waterbeds within the countryside and ultimately in the ocean. Alternatively, algae could play an important role in agriculture where they can be used as biofertilizers and soil stabilizers. To examine the possible reuse of the detritus generated by dead algae as fertilizer for crops, we develop three mathematical models building upon each other...
June 2017: Journal of Biological Physics
Sławomir Grzegorczyn, Andrzej Ślęzak, Brygida Przywara-Chowaniec
We analyzed the transport of KCl solutions through the bacterial cellulose membrane and concentration boundary layers (CBLs) near membrane with pressure differences on the membrane. The membrane was located in horizontal-plane between two chambers with different KCL solutions. The membrane was located in horizontal-plane between two chambers with different KCL solutions. As results from the elaborated model, gradient of KCL concentration in CBLs is maximal at membrane surfaces in the case when pressure difference on the membrane equals zero...
June 2017: Journal of Biological Physics
Naglaa M El-Sayed, Fifi M Reda, Omar F Farag, Doaa A Nasrallah
The influence of N2 plasma on the antibacterial properties of polystyrene/fullerene (C60/PS) nanocomposite films with two concentrations is investigated. A comparison is made between the surface characteristics of the films before and after plasma irradiation for different time intervals. The alterations induced on the surface of the films after treatment are analyzed by contact angle and surface energy measurements, FTIR spectroscopy, and atomic force microscopy. The antibacterial properties, growth, biofilm formation, and adhesion of the nanocomposite films against two multidrug-resistant bacterial strains, Staphylococcus aureus KT337489 and Pseudomonas aeruginosa KT337488, are investigated before and after plasma irradiation...
June 2017: Journal of Biological Physics
Ioannis G Karafyllidis
The very high light-harvesting efficiency of natural photosynthetic systems in conjunction with recent experiments, which showed quantum-coherent energy transfer in photosynthetic complexes, raised questions regarding the presence of non-trivial quantum effects in photosynthesis. Grover quantum search, quantum walks, and entanglement have been investigated as possible effects that lead to this efficiency. Here we explain the near-unit photosynthetic efficiency without invoking non-trivial quantum effects. Instead, we use non-equilibrium Green's functions, a mesoscopic method used to study transport in nano-conductors to compute the transmission function of the Fenna-Matthews-Olson (FMO) complex using an experimentally derived exciton Hamiltonian...
June 2017: Journal of Biological Physics
Ivana Pajic-Lijakovic, Milan Milivojevic
The mean features of cell surface rearrangement during cell aggregate rounding after uni-axial compression between parallel plates are considered. This is based on long-time rheological modeling approaches in order to shed further light on collective cell migration. Many aspects of cell migration at the supra-cellular level, such as the coordination between surrounding migrating cell groups that leads to uncorrelated motility, have remained unclear. Aggregate shape changes during rounding are considered depending on the size and homogeneity of 2-D and 3-D cell aggregates...
June 2017: Journal of Biological Physics
Roger Marrannes
No abstract text is available yet for this article.
June 2017: Journal of Biological Physics
Jordane Preto
Fröhlich's model equations describing phonon condensation in open systems of biological relevance are reinvestigated within a semi-classical statistical framework. The main assumptions needed to deduce Fröhlich's rate equations are identified and it is shown how they lead us to write an appropriate form for the corresponding master equation. It is shown how solutions of the master equation can be numerically computed and can highlight typical features of the condensation effect. Our approach provides much more information compared to the existing ones as it allows to investigate the time evolution of the probability density function instead of following single averaged quantities...
June 2017: Journal of Biological Physics
Viet Duc Nguyen, Toan T Nguyen, Paolo Carloni
Strongly correlated electrostatics of DNA systems has drawn the interest of many groups, especially the condensation and overcharging of DNA by multivalent counterions. By adding counterions of different valencies and shapes, one can enhance or reduce DNA overcharging. In this paper, we focus on the effect of multivalent co-ions, specifically divalent co-ions such as SO[Formula: see text]. A computational experiment of DNA condensation using Monte Carlo simulation in grand canonical ensemble is carried out where the DNA system is in equilibrium with a bulk solution containing a mixture of salt of different valency of co-ions...
June 2017: Journal of Biological Physics
Karim Mahnam, Fatame Raisi
Aspartame (L-Aspartyl-L-phenylalanine methyl ester) is a sweet dipeptide used in some foods and beverages. Experimental studies show that aspartame causes osteoporosis and some illnesses, which are similar to those of copper and calcium deficiency. This raises the issue that aspartame in food may interact with cations and excrete them from the body. This study aimed to study aspartame interaction with calcium, zinc, iron, sodium, and cadmium ions via molecular dynamics simulation (MD) and spectroscopy. Following a 480-ns molecular dynamics simulation, it became clear that the aspartame is able to sequester Fe(2+), Ca(2+), Cd(2+), and Zn(2+) ions for a long time...
March 2017: Journal of Biological Physics
Charles Deckard, Azida Walker, Brent J F Hill
It is well known that estrogen deficiency induces a deterioration of bone strength in aged females. The aim of this study is to determine the effect of estrogen depletion on tibia bone strength in sexually mature mice that are still undergoing skeletal maturation. At 8 weeks of age, C57BL/6 female mice underwent an ovariectomy (OVX) or sham (SHAM) surgery. Mice were killed at 2, 4, or 8 weeks post-surgery. Tibia length and cross-sectional area continued to increase in both treatment groups until 4 weeks post-surgery...
March 2017: Journal of Biological Physics
Zahra Sajjadiyan, Nasim Cheraghi, Sarah Mohammadinejad, Leila Hassani
Antibacterial peptides have potential as novel therapeutic agents for bacterial infections. Aurein 1.2 is one of the smallest antibacterial peptides extracted from an anuran. LLAA is a more active analogue of aurein 1.2. Antibacterial peptides usually accomplish their function by interacting with bacterial membrane selectively. In this study, we tried to find the reasons for the stronger antibacterial activity of LLAA compared with aurein 1.2. For this purpose, the interaction of aurein 1.2 and LLAA with dipalmitoylphosphatidylcholine (DPPC) was investigated by molecular dynamics (MD) simulation...
March 2017: Journal of Biological Physics
Haider Abbas
The nature of interaction between serine-a vital molecule for cancer cell proliferation and nucleic acid bases-adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U) is investigated within the framework of Møller-Plesset perturbation theory (MP2) and density functional theory (DFT). To quantify the interaction strength between serine and nucleobases, the corresponding binding energies were computed, showing energetic ordering such that G > C > T > A > U. This shows that the interaction energy of serine with guanine is the highest, while with uracil it is the lowest...
March 2017: Journal of Biological Physics
Yan-Jun Zhang, Jing-Na Ding, Hui Zhong, Chang-Ping Sun, Ju-Guang Han
VP35 of Ebola viruses (EBOVs) is an attractive potential target because of its multifunction. All-atom molecular dynamics (MD) simulations and Molecular Mechanics Generalized Born surface area (MM/GBSA) energy calculations are performed to investigate the single-walled carbon nanotube (SWCNT) as an inhibitor in wild-type (WT) VP35 as well as in three primary mutants (K248A, I295A, and K248A/I295A) through docking the SWCNT in the first basic patch (FBP) of VP35. The SWCNTs of all the four systems effectively bind to the FBP...
March 2017: Journal of Biological Physics
Željana Bonačić Lošić, Tomislav Donđivić, Davor Juretić
Triosephosphate isomerase (TIM) is often described as a fully evolved housekeeping enzyme with near-maximal possible reaction rate. The assumption that an enzyme is perfectly evolved has not been easy to confirm or refute. In this paper, we use maximization of entropy production within known constraints to examine this assumption by calculating steady-state cyclic flux, corresponding entropy production, and catalytic activity in a reversible four-state scheme of TIM functional states. The maximal entropy production (MaxEP) requirement for any of the first three transitions between TIM functional states leads to decreased total entropy production...
March 2017: Journal of Biological Physics
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