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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...
February 14, 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...
February 11, 2017: Journal of Biological Physics
Sonya Bahar
No abstract text is available yet for this article.
February 11, 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...
February 1, 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...
January 28, 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...
January 28, 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...
January 28, 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...
January 21, 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...
January 3, 2017: Journal of Biological Physics
Ludmila Yakushevich
The creation of mechanical analogues of biological systems is known as a useful instrument that helps to understand better the dynamical mechanisms of the functioning of living organisms. Mechanical analogues of biomolecules are usually constructed for imitation of their internal mobility, which is one of the most important properties of the molecules. Among the different types of internal motions, angular oscillations of nitrous bases are of special interest because they make a substantial contribution to the base pairs opening that in turn is an important element of the process of the DNA-protein recognition...
December 30, 2016: Journal of Biological Physics
Yuri M Yevdokimov, Sergey G Skuridin, Sergey V Semenov, Ljubov A Dadinova, Viktor I Salyanov, Efim I Kats
In this research, we observe and rationalize theoretically the transition from hexagonal to cholesteric packing of double-stranded (ds) DNA in dispersion particles. The samples were obtained by phase exclusion of linear ds DNA molecules from water-salt solutions of poly(ethylene glycol)-PEG-with concentrations ranging from 120 mg ml(-1) to 300 mg ml(-1). In the range of PEG concentrations from 120 mg ml(-1) to 220 mg ml(-1) at room temperature, we find ds DNA molecule packing, typical of classical cholesterics...
December 27, 2016: Journal of Biological Physics
Arkadiusz Bryll, Andrzej Ślęzak
In this paper, the authors investigate the membrane transport of aqueous non-electrolyte solutions in a single-membrane system with the membrane mounted horizontally. The purpose of the research is to analyze the influence of volume flows on the process of forming concentration boundary layers (CBLs). A mathematical model is provided to calculate dependences of a concentration polarization coefficient (ζ s ) on a volume flux (J vm ), an osmotic force (Δπ) and a hydrostatic force (ΔP) of different values...
November 12, 2016: Journal of Biological Physics
Maryam Ghahremani Nasab, Leila Hassani, Sara Mohammadi Nejad, Davood Norouzi
A DNA enzyme with peroxidase activity is a G-quadruplex-based DNAzyme formed by hemin and G-quadruplex DNA. Activity of peroxide DNAzymes can be influenced by the structure of quadruplex DNA. In this investigation, the interaction of hemin with T30695 G-quadruplex DNA is evaluated. Molecular dynamic simulation indicates that the binding mode of hemin to G-quadruplex DNA is end-stacking, which is consistent with absorption spectroscopy. Based on fluorescence spectroscopy, hemin ejects thiazole orange from bases of four-strand DNA...
October 17, 2016: Journal of Biological Physics
Leonor Cruzeiro, Léo Degrève
According to the thermodynamic hypothesis, the native state of proteins is uniquely defined by their amino acid sequence. On the other hand, according to Levinthal, the native state is just a local minimum of the free energy and a given amino acid sequence, in the same thermodynamic conditions, can assume many, very different structures that are as thermodynamically stable as the native state. This is the Levinthal limit explored in this work. Using computer simulations, we compare the interactions that stabilize the native state of four different proteins with those that stabilize three non-native states of each protein and find that the nature of the interactions is very similar for all such 16 conformers...
October 14, 2016: Journal of Biological Physics
Chongming Jiang, Chunyan Cui, Weirong Zhong, Gang Li, Li Li, Yuanzhi Shao
We study in silico the influence of host tissue inhomogeneity on tumor cell proliferation and diffusion by simulating the mobility of a tumor on percolation clusters with different homogeneities of surrounding tissues. The proliferation and diffusion of a tumor in an inhomogeneous tissue could be characterized in the framework of the percolation theory, which displays similar thresholds (0.54, 0.44, and 0.37, respectively) for tumor proliferation and diffusion in three kinds of lattices with 4, 6, and 8 connecting near neighbors...
October 2016: Journal of Biological Physics
S M Saberi Fathi
Knowledge regarding the 3D structure of a protein provides useful information about the protein's functional properties. Particularly, structural similarity between proteins can be used as a good predictor of functional similarity. One method that uses the 3D geometrical structure of proteins in order to compare them is the similarity value (SV). In this paper, we introduce a new definition of the SV measure for comparing two proteins. To this end, we consider the mass of the protein's atoms and concentrate on the number of protein's atoms to be compared...
October 2016: Journal of Biological Physics
Parvaneh Sayyad-Amin, Mohammad-Reza Jahansooz, Azam Borzouei, Fatemeh Ajili
Water shortage leads to a low quality of water, especially saline water in most parts of agricultural regions. This experiment was designed to determine the effects of saline irrigation on sorghum as a moderately salt-tolerant crop. To study salinity effects on photosynthetic pigment attributes including the chlorophyll content and chlorophyll fluorescence, an experiment was performed in a climate-controlled greenhouse at two vegetative and reproductive stages. The experimental design was factorial based on a completely randomized design with five NaCl concentrations (control, 50, 100, 150, and 200 mM), two grain and sweet-forage sorghum cultivars (Kimia and Pegah, respectively) and four replications...
October 2016: Journal of Biological Physics
I Nedkov, L Slavov, R Angelova, B Blagoev, D Kovacheva, M V Abrashev, M Iliev, V Groudeva
A detailed investigation of nanostructured iron oxides/(oxy)hydroxides gathered after cultivation of bacteria from the genus Leptothrix as iron (II) oxidizers is presented. A specific type of medium is selected for the cultivation of the bacteria. Results for sediment powder and bio-film on glass substrate samples from the same media are discussed. XRD, Raman spectroscopy, SEM, and TEM images and PPMS measurements are used to prove the exact composition of the biogenic products and to interpret the oxidation process...
October 2016: Journal of Biological Physics
Rudolf Podgornik
No abstract text is available yet for this article.
October 2016: Journal of Biological Physics
Mi Li, Lianqing Liu, Xiubin Xiao, Ning Xi, Yuechao Wang
Methotrexate is a commonly used anti-cancer chemotherapy drug. Cellular mechanical properties are fundamental parameters that reflect the physiological state of a cell. However, so far the role of cellular mechanical properties in the actions of methotrexate is still unclear. In recent years, probing the behaviors of single cells with the use of atomic force microscopy (AFM) has contributed much to the field of cell biomechanics. In this work, with the use of AFM, the effects of methotrexate on the viscoelastic properties of four types of cells were quantitatively investigated...
October 2016: Journal of Biological Physics
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