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Physical Review. E May 2021Protein complexes involved in DNA mismatch repair diffuse along dsDNA as sliding clamps in order to locate a hemimethylated incision site. They have been observed to use...
Protein complexes involved in DNA mismatch repair diffuse along dsDNA as sliding clamps in order to locate a hemimethylated incision site. They have been observed to use a dissociative mechanism, in which two proteins, while continuously remaining attached to the DNA, sometimes associate into a single complex sliding on the DNA and sometimes dissociate into two independently sliding proteins. Here, we study the probability that these complexes locate a given target site via a semi-analytic, Monte Carlo calculation that tracks the association and dissociation of the sliding complexes. We compare such probabilities to those obtained using a nondissociative diffusive scan in the space of physically realistic diffusion constants, hemimethylated site distances, and total search times to determine the regions in which dissociative searching is more or less efficient than nondissociative searching. We conclude that the dissociative search mechanism is advantageous in the majority of the physically realistic parameter space, suggesting that the dissociative search mechanism confers an evolutionary advantage.
Topics: DNA Mismatch Repair; Diffusion
PubMed: 34134264
DOI: 10.1103/PhysRevE.103.052404 -
ELife Jun 2024While inhomogeneous diffusivity has been identified as a ubiquitous feature of the cellular interior, its implications for particle mobility and concentration at...
While inhomogeneous diffusivity has been identified as a ubiquitous feature of the cellular interior, its implications for particle mobility and concentration at different length scales remain largely unexplored. In this work, we use agent-based simulations of diffusion to investigate how heterogeneous diffusivity affects the movement and concentration of diffusing particles. We propose that a nonequilibrium mode of membrane-less compartmentalization arising from the convergence of diffusive trajectories into low-diffusive sinks, which we call 'diffusive lensing,' is relevant for living systems. Our work highlights the phenomenon of diffusive lensing as a potentially key driver of mesoscale dynamics in the cytoplasm, with possible far-reaching implications for biochemical processes.
Topics: Diffusion; Biological Transport; Cytoplasm; Models, Biological; Cell Compartmentation; Computer Simulation
PubMed: 38896469
DOI: 10.7554/eLife.89794 -
Physical Review Letters Feb 2016Active fluids such as swarming bacteria and motile colloids exhibit exotic properties different from conventional equilibrium materials. As a peculiar example, a...
Active fluids such as swarming bacteria and motile colloids exhibit exotic properties different from conventional equilibrium materials. As a peculiar example, a spherical tracer immersed inside active fluids shows an enhanced translational diffusion, orders of magnitude stronger than its intrinsic Brownian motion. Here, rather than spherical tracers, we investigate the diffusion of isolated ellipsoids in a quasi-two-dimensional bacterial bath. Our study shows a nonlinear enhancement of both translational and rotational diffusions of ellipsoids. More importantly, we uncover an anomalous coupling between particles' translation and rotation that is strictly prohibited in Brownian diffusion. The coupling reveals a counterintuitive anisotropic particle diffusion, where an ellipsoid diffuses fastest along its minor axis in its body frame. Combining experiments with theoretical modeling, we show that such an anomalous diffusive behavior arises from the generic straining flow of swimming bacteria. Our work illustrates an unexpected feature of active fluids and deepens our understanding of transport processes in microbiological systems.
Topics: Bacterial Physiological Phenomena; Diffusion; Escherichia coli; Models, Biological; Suspensions
PubMed: 26919019
DOI: 10.1103/PhysRevLett.116.068303 -
IEEE Transactions on Nanobioscience Jan 2019Diffusive molecular communication (DMC) is one of the most promising approaches for realizing nano-scale communications in biological environments for healthcare...
Diffusive molecular communication (DMC) is one of the most promising approaches for realizing nano-scale communications in biological environments for healthcare applications. In this paper, a DMC system in biological cylindrical environment is considered, inspired by blood vessel structures in the body. The internal surface of the cylinder boundary is assumed to be covered by the biological receptors which may irreversibly react with hitting molecules. Also, the information molecules diffusing in the fluid medium are subject to a degradation reaction and flow. The concentration Green's function of diffusion in this environment is analytically derived which takes into account asymmetry in all radial, axial, and azimuthal coordinates. Employing obtained Green's function, information channel between transmitter and transparent receiver of DMC is characterized. To evaluate the DMC system in the biological cylinder, a simple on-off keying modulation scheme is adopted and corresponding error probability is derived. The particle-based simulation results confirm the proposed analysis. Also, the effect of different system parameters on the concentration Green's function are examined. Our results reveal that the degradation reaction and the boundary covered by biological receptors may be utilized to mitigate intersymbol interference and outperform the corresponding error probability.
Topics: Animals; Blood Vessels; Cell Communication; Cellular Microenvironment; Computer Simulation; Computers, Molecular; Diffusion; Models, Biological; Nanotechnology
PubMed: 30530368
DOI: 10.1109/TNB.2018.2885051 -
Scientific Reports Nov 2022The stability of natural convection in a vertical porous layer using a local thermal nonequilibrium model was first studied by Rees (Transp Porous Med 87:459-464, 2011)...
The stability of natural convection in a vertical porous layer using a local thermal nonequilibrium model was first studied by Rees (Transp Porous Med 87:459-464, 2011) following the proof of Gill (J Fluid Mech 35:545-547, 1969), called the Gill-Rees stability problem. The aim of the present study is to investigate the implication of an additional solute concentration field on the Gill-Rees problem. The stability eigenvalue problem is solved numerically and some novel results not observed in the studies of double-diffusive natural convection in vertical porous (local thermal equilibrium case) and non-porous layers are disclosed. The possibility of natural convection parallel flow in the basic state becoming unstable due to the addition of an extra diffusing component is established. In some cases, the neutral stability curves of stationary and travelling-wave modes are connected to form a loop within which the flow is unstable indicating the requirement of two thermal Darcy-Rayleigh numbers to specify the stability/instability criteria. Moreover, the change in the mode of instability is recognized in some parametric space. The results for the extreme cases of the scaled interphase heat transfer coefficient are discussed.
Topics: Animals; Gills; Diffusion; Convection; Porosity; Solutions
PubMed: 36369207
DOI: 10.1038/s41598-022-20966-2 -
Journal of Visualized Experiments : JoVE Sep 2018Diffusive convection (DC) occurs when the vertical stratified density is controlled by two opposing scalar gradients that have distinctly different molecular...
Diffusive convection (DC) occurs when the vertical stratified density is controlled by two opposing scalar gradients that have distinctly different molecular diffusivities, and the larger- and smaller- diffusivity scalar gradients have negative and positive contributions for the density distribution, respectively. The DC occurs in many natural processes and engineering applications, for example, oceanography, astrophysics and metallurgy. In oceans, one of the most remarkable features of DC is that the vertical temperature and salinity profiles are staircase-like structure, composed of consecutive steps with thick homogeneous convecting layers and relatively thin and high-gradient interfaces. The DC staircases have been observed in many oceans, especially in the Arctic and Antarctic Oceans, and play an important role on the ocean circulation and climatic change. In the Arctic Ocean, there exist basin-wide and persistent DC staircases in the upper and deep oceans. The DC process has an important effect on diapycnal mixing in the upper ocean and may significantly influence the surface ice-melting. Compared to the limitations of field observations, laboratory experiment shows its unique advantage to effectively examine the dynamic and thermodynamic processes in DC, because the boundary conditions and the controlled parameters can be strictly adjusted. Here, a detailed protocol is described to simulate the evolution process of DC staircase structure, including its generation, development and disappearance, in a rectangular tank filled with stratified saline water. The experimental setup, evolution process, data analysis, and discussion of results are described in detail.
Topics: Antarctic Regions; Arctic Regions; Climate Change; Convection; Diffusion; Ice Cover; Oceans and Seas; Salinity; Seawater; Temperature; Water Movements
PubMed: 30247476
DOI: 10.3791/58316 -
Nitric Oxide : Biology and Chemistry Feb 1997In this review, I consider the quantitative consequences of the diffusion of free NO in determining its biological actions. Several studies have measured the extent to... (Review)
Review
In this review, I consider the quantitative consequences of the diffusion of free NO in determining its biological actions. Several studies have measured the extent to which NO diffuses away from an NO-producing cell, and the distance of its diffusion is quite large, on the order of 100-200 microm. This wide diffusibility is consistent also with the high value for its diffusion constant, 3300 microm2/s. Mathematical simulations based on this wide diffusibility suggest that, within spatial limits of approximately 0.3-0.4 mm, the actions of free NO are dictated by the total number of NO-producing cells within this location as opposed to where the NO-producing cells are located within this space. These results suggest that the actions of NO are surprisingly long range and the diffusion of NO is an important determinant of its biological actions. Thus, the effects of NO on individual target cells may be determined more by each cell's preprogrammed characteristic response to NO than by proximity to an NO source. In addition, scavenging of NO by hemoglobin in blood vessels should represent a significant sink for its scavenging, posing difficulty for the postulate that only free NO functions as EDRF.
Topics: Animals; Diffusion; Models, Biological; Models, Chemical; Nitric Oxide
PubMed: 9701041
DOI: 10.1006/niox.1996.0112 -
Physical Review Letters Apr 2015Standard game theory cannot describe microbial interactions mediated by diffusible molecules. Nevertheless, we show that one can still model microbial dynamics using...
Standard game theory cannot describe microbial interactions mediated by diffusible molecules. Nevertheless, we show that one can still model microbial dynamics using game theory with parameters renormalized by diffusion. Contrary to expectations, greater sharing of metabolites reduces the strength of cooperation and leads to species extinction via a nonequilibrium phase transition. We report analytic results for the critical diffusivity and the length scale of species intermixing. Species producing slower public good is favored by selection when fitness saturates with nutrient concentration.
Topics: Diffusion; Ecosystem; Extinction, Biological; Microbial Interactions; Models, Biological
PubMed: 25955075
DOI: 10.1103/PhysRevLett.114.168102 -
Nature Communications Apr 2018Ionic transport through nanofluidic systems is a problem of fundamental interest in transport physics and has broad relevance in desalination, fuel cells, batteries,...
Ionic transport through nanofluidic systems is a problem of fundamental interest in transport physics and has broad relevance in desalination, fuel cells, batteries, filtration, and drug delivery. When the dimension of the fluidic system approaches the size of molecules in solution, fluid properties are not homogeneous and a departure in behavior is observed with respect to continuum-based theories. Here we present a systematic study of the transport of charged and neutral small molecules in an ideal nanofluidic platform with precise channels from the sub-microscale to the ultra-nanoscale (<5 nm). Surprisingly, we find that diffusive transport of nano-confined neutral molecules matches that of charged molecules, as though the former carry an effective charge. Further, approaching the ultra-nanoscale molecular diffusivities suddenly drop by up to an order of magnitude for all molecules, irrespective of their electric charge. New theoretical investigations will be required to shed light onto these intriguing results.
Topics: Diffusion; Hydrodynamics; Ions; Nanostructures; Nanotechnology; Particle Size; Rheology; Surface Properties
PubMed: 29703954
DOI: 10.1038/s41467-018-04133-8 -
Journal of Environmental Management Jan 2023Significant amounts of heat can be generated during the initial stages after wastes are deposited in landfills, primarily due to decomposition of food waste. Objectives... (Review)
Review
Significant amounts of heat can be generated during the initial stages after wastes are deposited in landfills, primarily due to decomposition of food waste. Objectives of this study are to compile, examine and compare thermal properties of municipal solid waste (MSW) components, and liquid and gas phases in MSW landfills and their thermal responses that effect temperature increases in gas and leachate. Specific thermal properties examined include thermal conductivity, thermal diffusivity, and specific heat of waste materials deposited in landfills, liquids (water), and gases present. Compilation of these properties will allow in depth thermal analyses to evaluate heat transfer dynamics in landfills with different waste compositions. Examination of thermal characteristics of MSW components indicate that heat generated during decomposition of waste components would primarily be transferred to liquid (leachate) due to formation of water and gaseous components and their high specific heats. As a result, both the leachate and gases released from a landfill during the initial stages after wastes are deposited and when some oxygen is present as an electron acceptor will be warmer. Except for the metals and construction waste, it is likely that most waste components will have a significant temperature gradient during warming up and cooling off stages due to their low thermal conductivities and low thermal diffusivities. Even when the gas phase is at higher temperatures, it will take long time for waste materials (other than food waste and metals) to come to a uniform temperature during the heat generation (primarily due to decomposition of food waste) in a landfill.
Topics: Solid Waste; Refuse Disposal; Hot Temperature; Food; Thermal Diffusion; Waste Disposal Facilities; Gases; Water
PubMed: 36343401
DOI: 10.1016/j.jenvman.2022.116651