Two-Phase Dynamics of DNA Supercoiling Based on DNA Polymer Physics Model

SUMMARYHeat-induced gelation of milk was studied using both rheological and structural techniques. The sample was a conventional skim milk, concentrated with an ultrafiltration membrane, which formed gels when heated at appropriate pH. We investigated some factors that are considered to affect the gelation, such as concentration, pH and rennet treatment. The gelation process was monitored with a high precision oscillatory shear rheometer and the structure of gels was evaluated with quasi-elastic laser light scattering. From these results the gelation and phase separation behaviour were determined. By combining the results for different concentrations a phase diagram was obtained, which indicated that skim milk had a two-phase region on the higher temperature side. The effects of pH and rennet treatment were also evaluated with the aid of this phase diagram. The results were discussed on the basis of concepts of the phase behaviour of polymers, which were successfully developed in polymer physics.

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On the transition between turbulence regimes in particle-laden channel flows

Journal of Fluid Mechanics ◽

10.1017/jfm.2018.259 ◽

2018 ◽

Vol 845 ◽

pp. 499-519 ◽

Cited By ~ 22

Author(s):

Jesse Capecelatro ◽

Olivier Desjardins ◽

Rodney O. Fox

Keyword(s):

Reynolds Number ◽

Fluid Phase ◽

Stokes Number ◽

Channel Flows ◽

High Mass ◽

Inertial Particles ◽

Mass Loading ◽

Two Phase ◽

Phase Dynamics ◽

Wide Range

Turbulent wall-bounded flows exhibit a wide range of regimes with significant interaction between scales. The fluid dynamics associated with single-phase channel flows is predominantly characterized by the Reynolds number. Meanwhile, vastly different behaviour exists in particle-laden channel flows, even at a fixed Reynolds number. Vertical turbulent channel flows seeded with a low concentration of inertial particles are known to exhibit segregation in the particle distribution without significant modification to the underlying turbulent kinetic energy (TKE). At moderate (but still low) concentrations, enhancement or attenuation of fluid-phase TKE results from increased dissipation and wakes past individual particles. Recent studies have shown that denser suspensions significantly alter the two-phase dynamics, where the majority of TKE is generated by interphase coupling (i.e. drag) between the carrier gas and clusters of particles that fall near the channel wall. In the present study, a series of simulations of vertical particle-laden channel flows with increasing mass loading is conducted to analyse the transition from the dilute limit where classical mean-shear production is primarily responsible for generating fluid-phase TKE to high-mass-loading suspensions dominated by drag production. Eulerian–Lagrangian simulations are performed for a wide range of particle loadings at two values of the Stokes number, and the corresponding two-phase energy balances are reported to identify the mechanisms responsible for the observed transition.

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Modeling and controlling the two-phase dynamics of the p53 network: a Boolean network approach

New Journal of Physics ◽

10.1088/1367-2630/16/12/125010 ◽

2014 ◽

Vol 16 (12) ◽

pp. 125010 ◽

Cited By ~ 9

Author(s):

Guo-Qiang Lin ◽

Bin Ao ◽

Jia-Wei Chen ◽

Wen-Xu Wang ◽

Zeng-Ru Di

Keyword(s):

Boolean Network ◽

Network Approach ◽

Two Phase ◽

Phase Dynamics ◽

P53 Network

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Complex network analysis of phase dynamics underlying oil-water two-phase flows

Scientific Reports ◽

10.1038/srep28151 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 3

Author(s):

Zhong-Ke Gao ◽

Shan-Shan Zhang ◽

Qing Cai ◽

Yu-Xuan Yang ◽

Ning-De Jin

Keyword(s):

Network Analysis ◽

Complex Network ◽

Two Phase Flows ◽

Two Phase ◽

Phase Dynamics ◽

Complex Network Analysis ◽

Oil Water

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Simulation of the absorption of gaseous SO2 by fog droplets using a refined interpolation-sectional droplet model

Кибернетика и программирование ◽

10.25136/2644-5522.2020.2.33914 ◽

2020 ◽

pp. 19-32

Author(s):

Vladimir Viktorovich Pekunov

Keyword(s):

Numerical Simulation ◽

Mathematical Model ◽

Sulfur Dioxide ◽

Road Transport ◽

Two Phase ◽

Phase Dynamics ◽

Lagrangian Modeling ◽

Gaseous Sulfur ◽

Kinetics Of ◽

Droplet Phase

This article examines the problem of numerical simulation of interaction between the gaseous sulfur dioxide emitted by road transport and fog in the conditions of high humidity. For this purpose, the author applies a multi-factor two-phase mathematical model, which takes into account the dynamics of turbulent main phase, dynamics and kinetics of the multi-sectional droplet phase, presence of thermal inconsistencies formed as a result of direct and diffused solar radiation in various ranges, diffusion of sulfur dioxide, and its absorption by the fog droplets. The article carries out a numerical calculation of the corresponding task within the modeling system of environmental processes AirEcology-P, which allows generating the optimal calculation code for a particular mathematical model. The proposed complex mathematical model that descries interaction between the emitted sulfur dioxide gas and the fog droplets is new; it specifies the calculation of the kinetics of droplet phase based on consideration of the additional factor of droplet fusion characteristic to fog. The submodel of the droplet phase was tested in the numerical simulation (the results were compared with the data of direct Lagrangian modeling of the composite of 1,000 droplets), indicating decent accuracy results. The article obtains the results of numerical simulation of interaction between the emitted SO2 and the droplets. The author demonstrates the self-cleaning ability of the atmosphere, the degree of which correlates with the initial concentration of the smallest droplets and the height from the surface.

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Зміни електрогіпокампограми та поведінкових реакцій щурів при посиленні протягом тривалого стресу ГАМК-ергічних механізмів мозку

Visnyk of Dnipropetrovsk University Biology medicine ◽

10.15421/021209 ◽

2012 ◽

Vol 3 (1) ◽

pp. 62-69

Author(s):

O. Z. Мelnikova ◽

V. P. Lyashenko

Keyword(s):

Spectral Composition ◽

Behavioral Reactions ◽

Two Phase ◽

Phase Dynamics ◽

Brain Gaba ◽

Prolonged Stress

The changes of waves’ power and spectral composition of electrohippocampogram (EHpG) were analyzed in rats which brain GABA-ergic mechanisms increased by gidazepam and pyracetam during prolonged stress comparatively to the indices of EHpG under isolated affective influence. The nature of two-phase dynamics of the changes could indicate an adaptogenic action of drugs. It’s shown that modulation of central processes during prolonged stress and amplification of brain GABA-ergic mechanisms are accompanied by the changes of the animals’ behavioral reactions.

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RNA structure prediction including pseudoknots through direct enumeration of states

10.1101/338921 ◽

2018 ◽

Author(s):

Ofer Kimchi ◽

Tristan Cragnolini ◽

Michael P. Brenner ◽

Lucy J. Colwell

Keyword(s):

Rna Structure ◽

Structure Prediction ◽

Secondary Structures ◽

Polymer Physics ◽

Rna Sequences ◽

Rna Structure Prediction ◽

Order Of Magnitude ◽

Np Complete ◽

Physics Model ◽

Physical Quantities

The accurate prediction of RNA secondary structure from primary sequence has had enormous impact on research from the past forty years. While many algorithms are available to make these predictions, the inclusion of non-nested loops, termed pseudoknots, still poses challenges. Here, we describe a new method to compute the entire free energy landscape of secondary structures of RNA resulting from a primary RNA sequence, by combining a polymer physics model for the entropy of pseudoknots with exhaustive enumeration of the set of possible structures. Our polymer physics model can address arbitrarily complex pseudoknots and has only two free loop entropy parameters that correspond to concrete physical quantities, over an order of magnitude fewer than even the sparsest state-of-the-art algorithms. Our model outperforms previously published methods in predicting pseudoknots, while performing on par with current methods in the prediction of non-pseudoknotted structures. For RNA sequences of ~ 45 nucleotides, or ~ 90 with minimal heuristics, the complet–e enumeration of possible secondary structures can be accomplished quickly despite the NP-complete nature of the problem.

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