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Connor Jernigan posted an update 6 months ago
The prevailing theories describing DNA confinement in a nanochannel are predicated on the assumption that wall-DNA electrostatic interactions are sufficiently short-ranged such that the problem can be mapped to an equivalent neutral polymer confined by hard walls with an appropriately reduced effective channel size. To determine when this hypothesis is valid, we leveraged a recently reported experimental data set for the fractional extension of DNA molecules in a 250-nm-wide poly(dimethyl siloxane) (PDMS) nanochannel with buffer ionic strengths between 0.075 and 48 mM. Evaluating these data in the context of the weakly correlated telegraph model of DNA confinement reveals that, at ionic strengths greater than 0.3 mM, the average fractional extension of the DNA molecules agree with theoretical predictions with a mean absolute error of 0.04. In contrast, experiments at ionic strengths below 0.3 mM produce average fractional extensions that are systematically smaller than the theoretical predictions with a larger mean absolute error of 0.15. The deviations between experiment and theory display a correlation coefficient of 0.82 with the decay length for the DNA-wall electrostatics, linking the deviations with a breakdown in approximating the DNA with an equivalent neutral polymer.In the present paper, we theoretically study the drag force on nanoparticles in the free-molecule regime. It has been widely assumed that the particle temperature is equal to the gas media temperature in the open literature. However, this assumption can be invalid in some real applications. Based on the kinetic theory, we obtain the generalized formulas for the drag force on nanoparticles in the free-molecule regime. It is found that there exists a significant error induced by the assumption of equal temperature between the particle and the surrounding gas. Therefore, it is necessary to consider the effect of the particle temperature in the analysis of the particle transport properties.I study the equilibrium and nonequilibrium dynamics of a conservative and reversible Q2R cellular automata. This system exhibits a configuration space with 2^2N states, which grows with the size of the system. In this context, for small size, the phase space has fixed points and cycles. Through numerical studies and using a statistical approach, I can observe stable and unstable behaviors as well as a phase transition around a critical energy E_c. I introduce a coupling constant as a perturbation to the classic Q2R model and show through the phase diagram how this modified model exhibits three different phases.In this paper, we develop a conservative phase-field method for interface-capturing among N (N≥2) immiscible fluids, the evolution of the fluid-fluid interface is captured by conservative Allen-Cahn equation (CACE), and the interface force of N immiscible fluids is incorporated to Navier-Stokes equation (NSE) by chemical potential form. Accordingly, we propose a lattice Boltzmann equation (LBE) method for solving N (N≥2) immiscible incompressible NSE and CACE at high density and viscosity contrasts. Numerical simulations including stationary droplets, Rayleigh-Taylor instability, spreading of liquid lenses, and spinodal decompositions are carried out to show the accuracy and capability of present LBE, and the results show that the predictions by use of the present LBE agree well with the analytical solutions and/or other numerical results.We examine the behavior of supercoiled DNA minicircles containing between 200 and 400 base-pairs, also named microDNA, in which supercoiling favors thermally assisted DNA denaturation bubbles of nanometer size and controls their lifetime. Mesoscopic modeling and accelerated dynamics simulations allow us to overcome the limitations of atomistic simulations encountered in such systems, and offer detailed insight into the thermodynamic and dynamical properties associated with the nucleation and closure mechanisms of long-lived thermally assisted denaturation bubbles which do not stem from bending- or torque-driven stress. Suitable tuning of the degree of supercoiling and size of specifically designed microDNA is observed to lead to the control of opening characteristic times in the millisecond range, and closure characteristic times ranging over well distinct timescales, from microseconds to several minutes. We discuss how our results can be seen as a dynamical bandwidth which might enhance selectivity for specific DNA binding proteins.We develop a dynamic mean-field theory for polar active particles that interact through a self-generated field, in particular one generated through emitting a chemical signal. While being a form of chemotactic response, it is different from conventional chemotaxis in that particles discontinuously change their motility when the local concentration surpasses a threshold. The resulting coupled equations for density and polarization are linear and can be solved analytically for simple geometries, yielding inhomogeneous density profiles. Specifically, here we consider a planar and circular interface. read more Our theory thus explains the observed coexistence of dense aggregates with an active gas. There are, however, differences from the more conventional picture of liquid-gas coexistence based on a free energy, most notably the absence of a critical point. We corroborate our analytical predictions by numerical simulations of active particles under confinement and interacting through volume exclusion. Excellent quantitative agreement is reached through an effective translational diffusion coefficient. We finally show that an additional response to the chemical gradient direction is sufficient to induce vortex clusters. Our results pave the way to engineer motility responses in order to achieve aggregation and collective behavior even at unfavorable conditions.Effects of mechanical coupling on cardiac dynamics are studied by monitoring the beating dynamics of a cardiac tissue which is being pulled periodically at a pace slower than its intrinsic beating rate. The tissue is taken from the heart of a bullfrog that includes pacemaker cells. The cardiac tissue beats spontaneously with an almost constant interbeat interval (IBI) when there is no external forcing. On the other hand, the IBI is observed to vary significantly under an external periodic drive. Interestingly, when the period of the external drive is about two times the intrinsic IBI of the tissue without pulling, the IBI as a function of time exhibits a wave packet structure. Our experimental results can be understood theoretically by a phase-coupled model under external driving. In particular, the theoretical prediction of the wave-packet period as a function of the normalized driving period agrees excellently with the observations. Furthermore, the cardiac mechanical coupling constant can be extracted from the experimental data from our model and is found to be insensitive to the external driving period.
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