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Journal of Biological Physics

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https://www.readbyqxmd.com/read/28378262/quantum-transport-in-the-fmo-photosynthetic-light-harvesting-complex
#1
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...
April 4, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28337554/successive-relaxation-cycles-during-long-time-cell-aggregate-rounding-after-uni-axial-compression
#2
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...
March 23, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28321631/erratum-to-computer-model-of-unstirred-layer-and-intracellular-ph-changes-determinants-of-unstirred-layer-ph
#3
Roger Marrannes
No abstract text is available yet for this article.
March 20, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28197797/semi-classical-statistical-description-of-fr%C3%A3-hlich-condensation
#4
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
https://www.readbyqxmd.com/read/28190162/dna-like-charge-attraction-and-overcharging-by-divalent-counterions-in-the-presence-of-divalent-co-ions
#5
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
https://www.readbyqxmd.com/read/28188566/review-of-the-physics-of-living-systems-by-fabrizio-cleri-springer-2016-620-pp-isbn-978-3-319-30645-2
#6
Sonya Bahar
No abstract text is available yet for this article.
March 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28150114/a-theoretical-and-experimental-study-of-calcium-iron-zinc-cadmium-and-sodium-ions-absorption-by-aspartame
#7
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
https://www.readbyqxmd.com/read/28132161/using-three-point-bending-to-evaluate-tibia-bone-strength-in-ovariectomized-young-mice
#8
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
https://www.readbyqxmd.com/read/28130642/interaction-of-aurein-1-2-and-its-analogue-with-dppc-lipid-bilayer
#9
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
https://www.readbyqxmd.com/read/28130641/first-principles-study-of-interaction-of-serine-with-nucleobases-of-dna-and-rna
#10
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
https://www.readbyqxmd.com/read/28110448/molecular-dynamics-exploration-of-the-binding-mechanism-and-properties-of-single-walled-carbon-nanotube-to-wt-and-mutant-vp35-fbp-region-of-ebola-virus
#11
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
https://www.readbyqxmd.com/read/28050739/is-the-catalytic-activity-of-triosephosphate-isomerase-fully-optimized-an-investigation-based-on-maximization-of-entropy-production
#12
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
https://www.readbyqxmd.com/read/28039557/on-the-mechanical-analogue-of-dna
#13
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...
March 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28028733/re-entrant-cholesteric-phase-in-dna-liquid-crystalline-dispersion-particles
#14
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...
March 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/27838811/the-mathematical-model-of-concentration-polarization-coefficient-in-membrane-transport-and-volume-flows
#15
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...
March 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/27752804/interaction-of-hemin-with-quadruplex-dna
#16
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...
March 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/27743150/exploring-the-levinthal-limit-in-protein-folding
#17
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...
March 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/27678112/tumor-proliferation-and-diffusion-on-percolation-clusters
#18
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
https://www.readbyqxmd.com/read/27623799/a-new-definition-and-properties-of-the-similarity-value-between-two-protein-structures
#19
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
https://www.readbyqxmd.com/read/27586195/changes-in-photosynthetic-pigments-and-chlorophyll-a-fluorescence-attributes-of-sweet-forage-and-grain-sorghum-cultivars-under-salt-stress
#20
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
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