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Journal of Biological Physics

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https://www.readbyqxmd.com/read/28929407/gibbs-free-energy-as-a-measure-of-complexity-correlates-with-time-within-c-elegans-embryonic-development
#1
Samuel H McGuire, Edward A Rietman, Hava Siegelmann, Jack A Tuszynski
We investigate free energy behavior in the nematode Caenorhabditis elegans during embryonic development. Our approach utilizes publicly available gene expression data, which gives us a picture of developmental changes in protein concentration and, resultantly, chemical potential and free energy. Our results indicate a clear global relationship between Gibbs free energy and time spent in development and provide thermodynamic indicators of the large-scale biological events of cell division and differentiation...
September 19, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28914402/analytical-modeling-of-the-mechanics-of-early-invasion-of-a-merozoite-into-a-human-erythrocyte
#2
Tamer Abdalrahman, Thomas Franz
In this study, we used a continuum model based on contact mechanics to understand the mechanics of merozoite invasion into human erythrocytes. This model allows us to evaluate the indentation force and work as well as the contact pressure between the merozoite and erythrocyte for an early stage of invasion (γ = 10%). The model predicted an indentation force of 1.3e (-11)N and an indentation work of 1e (-18)J. The present analytical model can be considered as a useful tool not only for investigations in mechanobiology and biomechanics but also to explore novel therapeutic targets for malaria and other parasite infections...
September 15, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28913768/ionic-effects-on-the-temperature-force-phase-diagram-of-dna
#3
Sitichoke Amnuanpol
Double-stranded DNA (dsDNA) undergoes a structural transition to single-stranded DNA (ssDNA) in many biologically important processes such as replication and transcription. This strand separation arises in response either to thermal fluctuations or to external forces. The roles of ions are twofold, shortening the range of the interstrand potential and renormalizing the DNA elastic modulus. The dsDNA-to-ssDNA transition is studied on the basis that dsDNA is regarded as a bound state while ssDNA is regarded as an unbound state...
September 14, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28900825/frequency-associated-transition-from-single-cell-asynchronous-motion-to-monotonic-growth
#4
Marcin Lipowczan, Mariusz Pietruszka
This paper presents a Fourier analysis of the Ortega equation that examines the growth dynamics of plants, specifically the pollen tubes or non-meristematic zones of elongating coleoptiles. A frequency-induced transition from highly nonlinear (periodical) growth-like the one observed in pollen tubes-to monotonically ascending and asymptotically saturated (sigmoid-like) growth, which is anticipated within the framework of a 'two-fluid model', is shown. A dynamic phase diagram is calculated and presented in the form of a live video clip...
September 12, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28887655/freezing-shortens-the-lifetime-of-dna-molecules-under-tension
#5
Wei-Ju Chung, Yujia Cui, Chi-Shuo Chen, Wesley H Wei, Rong-Shing Chang, Wun-Yi Shu, Ian C Hsu
DNA samples are commonly frozen for storage. However, freezing can compromise the integrity of DNA molecules. Considering the wide applications of DNA molecules in nanotechnology, changes to DNA integrity at the molecular level may cause undesirable outcomes. However, the effects of freezing on DNA integrity have not been fully explored. To investigate the impact of freezing on DNA integrity, samples of frozen and non-frozen bacteriophage lambda DNA were studied using optical tweezers. Tension (5-35 pN) was applied to DNA molecules to mimic mechanical interactions between DNA and other biomolecules...
September 8, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28879538/persistence-length-of-collagen-molecules-based-on-nonlocal-viscoelastic-model
#6
Esmaeal Ghavanloo
Persistence length is one of the most interesting properties of a molecular chain, which is used to describe the stiffness of a molecule. The experimentally measured values of the persistence length of the collagen molecule are widely scattered from 14 to 180 nm. Therefore, an alternative approach is highly desirable to predict the persistence length of a molecule and also to explain the experimental results. In this paper, a nonlocal viscoelastic model is developed to obtain the persistence length of the collagen molecules in solvent...
September 6, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28875391/dynamics-of-rebounding-bacillus-subtilis-spores-determined-using-image-charge-detection
#7
Brandon L Barney, Daniel E Austin
A novel image-charge detection technique was used to investigate the mechanical elasticity of bare bacterial spores during high-velocity impact. Spores of Bacillus subtilis introduced to vacuum using electrospray and aerodynamic acceleration impacted and rebounded off of a glass plate. A dual-stage, asymmetric image-charge detector measured the velocity and direction of each spore both before and after impact with the glass surface. Two ranges of impact velocity were investigated, with average initial velocities of 197 ± 17 and 145 ± 12 m/s...
September 5, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28780598/optimization-of-monomethoxy-polyethyleneglycol-modified-oxalate-decarboxylase-by-response-surface-methodology
#8
Han Long, XingHua Cai, Hui Yang, JunBin He, Jia Wu, RiHui Lin
In order to improve the stability of oxalate decarboxylase (Oxdc), response surface methodology (RSM), based on a four-factor three-level Box-Behnken central composite design was used to optimize the reaction conditions of oxalate decarboxylase (Oxdc) modified with monomethoxy polyethyleneglycol (mPEG5000). Four independent variables such as the ratio of mPEG-aldehyde to Oxdc, reaction time, temperature, and reaction pH were investigated in this work. The structure of modified Oxdc was identified by sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and Fourier transform infrared (FTIR) spectroscopy, the stability of the modified Oxdc was also investigated...
August 5, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28752254/interaction-between-c18-fatty-acids-and-dope-peg2000-in-langmuir-monolayers-effect-of-degree-of-unsaturation
#9
Lai Ti Gew, Misni Misran
In this study, we address the effect of the cis-double bond in 1,2-dioleoyl-sn-glycero-3-phosphoethanolamide-N-[methoxy(polyethylene glycol)-2000, DOPE PEG2000 (DP), on the Langmuir monolayer of C18 fatty acids-namely, stearic acid (SA), oleic acid (L1), linoleic acid (L2), and linolenic acid (L3)-with the same head group but different degrees of saturation on their hydrocarbon chains. Negative values of Gibbs free energy of mixing (ΔG mix) were obtained throughout the investigated ranges of the unsaturated C18 fatty-acid (L1, L2 and L3) mixed systems, indicating that very strong attractions occurred between molecules in the monolayers...
July 27, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28730355/charge-transport-in-dna-model-with-vibrational-and-rotational-coupling-motions
#10
H Ngoubi, G H Ben-Bolie, T C Kofané
The dynamics of the Peyrard-Bishop model for vibrational motion of DNA dynamics, which has been extended by taking into account the rotational motion for the nucleotides (Silva et al., J. Biol. Phys. 34, 511-519, 2018) is studied. 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. We show that the original differential-difference equation for the DNA dynamics can be reduced in the continuum approximation to a set of three coupled nonlinear equations...
July 20, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28707197/quantum-like-behavior-without-quantum-physics-i-kinematics-of-neural-like-systems
#11
S A Selesnick, J P Rawling, Gualtiero Piccinini
Recently there has been much interest in the possible quantum-like behavior of the human brain in such functions as cognition, the mental lexicon, memory, etc., producing a vast literature. These studies are both empirical and theoretical, the tenets of the theory in question being mainly, and apparently inevitably, those of quantum physics itself, for lack of other arenas in which quantum-like properties are presumed to obtain. However, attempts to explain this behavior on the basis of actual quantum physics going on at the atomic or molecular level within some element of brain or neuronal anatomy (other than the ordinary quantum physics that underlies everything), do not seem to survive much scrutiny...
July 13, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28664286/direct-measurement-of-interaction-forces-between-a-platinum-dichloride-complex-and-dna-molecules
#12
Hiroshi Muramatsu, Shogo Shimada, Tomoko Okada
The interaction forces between a platinum dichloride complex and DNA molecules have been studied using atomic force microscopy (AFM). The platinum dichloride complex, di-dimethylsulfoxide-dichloroplatinum (II) (Pt(DMSO)2Cl2), was immobilized on an AFM probe by coordinating the platinum to two amino groups to form a complex similar to Pt(en)Cl2, which is structurally similar to cisplatin. The retraction forces were measured between the platinum complex and DNA molecules immobilized on mica plates using force curve measurements...
June 29, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28647778/a-correlation-between-secondary-structure-and-rheological-properties-of-low-density-lipoproteins-at-air-water-interfaces
#13
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
https://www.readbyqxmd.com/read/28647777/the-effect-of-low-and-high-power-microwave-irradiation-on-in-vitro-grown-sequoia-plants-and-their-recovery-after-cryostorage
#14
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
https://www.readbyqxmd.com/read/28577238/dihedral-angle-preferences-of-amino-acid-residues-forming-various-non-local-interactions-in-proteins
#15
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
https://www.readbyqxmd.com/read/28567598/the-interplay-between-phenotypic-and-ontogenetic-plasticities-can-be-assessed-using-reaction-diffusion-models-the-case-of-pseudoplatystoma-fishes
#16
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
https://www.readbyqxmd.com/read/28555360/a-correlation-between-long-term-in-vitro-dynamic-calcification-and-abnormal-flow-patterns-past-bioprosthetic-heart-valves
#17
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
https://www.readbyqxmd.com/read/28550636/the-role-of-algae-in-agriculture-a-mathematical-study
#18
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
https://www.readbyqxmd.com/read/28500449/concentration-polarization-phenomenon-in-the-case-of-mechanical-pressure-difference-on-the-membrane
#19
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
https://www.readbyqxmd.com/read/28474135/surface-analysis-of-nitrogen-plasma-treated-c60-ps-nanocomposite-films-for-antibacterial-activity
#20
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
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