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Journal of Biological Physics

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https://www.readbyqxmd.com/read/29134490/knot-soliton-in-dna-and-geometric-structure-of-its-free-energy-density
#1
Ying Wang, Xuguang Shi
In general, the geometric structure of DNA is characterized using an elastic rod model. The Landau model provides us a new theory to study the geometric structure of DNA. By using the decomposition of the arc unit in the helical axis of DNA, we find that the free-energy density of DNA is similar to the free-energy density of a two-condensate superconductor. By using the φ-mapping topological current theory, the torus knot soliton hidden in DNA is demonstrated. We show the relation between the geometric structure and free-energy density of DNA and the Frenet equations in differential geometry theory are considered...
November 13, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/29124623/removal-of-ligand-bound-liposomes-from-cell-surfaces-by-microbubbles-exposed-to-ultrasound
#2
Stuart Ibsen, Ruben Mora, Guixin Shi, Carolyn Schutt, Wenjin Cui, Michael Benchimol, Viviana Serra, Sadik Esener
Gas-filled microbubbles attached to cell surfaces can interact with focused ultrasound to create microstreaming of nearby fluid. We directly observed the ultrasound/microbubble interaction and documented that under certain conditions fluorescent particles that were attached to the surface of live cells could be removed. Fluorescently labeled liposomes that were larger than 500 nm in diameter were attached to the surface of endothelial cells using cRGD targeting to αvβ3 integrin. Microbubbles were attached to the surface of the cells through electrostatic interactions...
November 9, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/29090363/calcium-axonemal-microtubuli-interactions-underlie-mechanism-s-of-primary-cilia-morphological-changes
#3
Vlado A Buljan, Manuel B Graeber, R M Damian Holsinger, Daniel Brown, Brett D Hambly, Edward J Delikatny, Vladimira R Vuletic, Xavier N Krebs, Ilijan B Tomas, John J Bohorquez-Florez, Guo Jun Liu, Richard B Banati
We have used cell culture of astrocytes aligned within microchannels to investigate calcium effects on primary cilia morphology. In the absence of calcium and in the presence of flow of media (10 μL.s(-1)) the majority (90%) of primary cilia showed reversible bending with an average curvature of 2.1 ± 0.9 × 10(-4) nm(-1). When 1.0 mM calcium was present, 90% of cilia underwent bending. Forty percent of these cilia demonstrated strong irreversible bending, resulting in a final average curvature of 3...
October 31, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/29027614/statistical-crossover-and-nonextensive-behavior-of-neuronal-short-term-depression
#4
A J da Silva, S Floquet, D O C Santos
The theoretical basis of neuronal coding, associated with short-term degradation in synaptic transmission, is a matter of debate in the literature. In fact, electrophysiological signals are commonly characterized as inversely proportional to stimulus intensity. Among theoretical descriptions of this phenomenon, models based on 1/f-dependency are employed to investigate the biophysical properties of short-term synaptic depression. In this work, we formulate a model based on a paradigmatic q-differential equation to obtain a generalized formalism useful for investigation of nonextensivity in this specific type of synaptic plasticity...
October 13, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/29019071/protein-actions-principles-and-modeling-by-i-bahar-r-l-jernigan-and-k-a-dill-garland-science-taylor-francis-group-1st-edition-feb-09-2017-isbn-9780815341772
#5
https://www.readbyqxmd.com/read/29019015/conformations-of-a-charged-vesicle-interacting-with-an-oppositely-charged-particle
#6
Hua Duan, Jianfeng Li, Hongdong Zhang, Feng Qiu, Yuliang Yang
Endocytotic and exocytotic processes are usually studied using particle-vesicle systems in theory, but most of them are electroneutral. Nevertheless, charged particle-vesicle systems are much closer to real biological systems. Therefore, wrapping behaviors of a negatively charged vesicle wrapping a positively charged particle are systematically investigated by a series of 2D dynamical simulations in this article. The competition between the elastic bending energy and the electrostatic energy dictates the vesicle configuration and charge distribution...
October 10, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28988403/deterministic-and-stochastic-analysis-of-an-eco-epidemiological-model
#7
Chandan Maji, Debasis Mukherjee, Dipak Kesh
Chronic wasting disease (CWD) is a contagious prion disease among the deer family that has the potential to disrupt the ecosystems where deer occur in abundance. To understand the dynamics of this emerging infectious disease, we consider a simple eco-epidemic model where the host population is infected by CWD. Boundedness of the system is established. The structure of equilibria and their linearized stability are investigated. The persistence condition is discussed. By constructing a suitable Lyapunov function, we discuss the global stability of the endemic equilibrium...
October 7, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28983809/temperature-evolution-of-trp-cage-folding-pathways-an-analysis-by-dividing-the-probability-flux-field-into-stream-tubes
#8
Vladimir A Andryushchenko, Sergei F Chekmarev
Owing to its small size and very fast folding rate, the Trp-cage miniprotein has become a benchmark system to study protein folding. Two folding pathways were found to be characteristic of this protein: pathway I, in which the hydrophobic collapse precedes the formation of α-helix, and pathway II, in which the events occur in the reverse order. At the same time, the relative contribution of these pathways at different temperatures as well as the nature of transition from one pathway to the other remain unclear...
October 5, 2017: Journal of Biological Physics
https://www.readbyqxmd.com/read/28929407/gibbs-free-energy-as-a-measure-of-complexity-correlates-with-time-within-c-elegans-embryonic-development
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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