Search results for "Quantitative Biology::Subcellular Processes"
showing 10 items of 97 documents
Current rectification by nanoparticle blocking in single cylindrical nanopores.
2014
Blocking of a charged pore by an oppositely charged nanoparticle can support rectifying properties in a cylindrical nanopore, as opposed to the usual case of a fixed asymmetry in the pore geometry and charge distribution. We present here experimental data and model calculations to confirm this fundamental effect. The nanostructure imaging and the effects of nanoparticle concentration, pore radius, and salt concentration on the electrical conductance–voltage (G–V) curves are discussed. Logic responses based on chemical and electrical inputs/outputs could also be implemented with a single pore acting as an effective nanofluidic diode. To better show the generality of the results, different ch…
Monte Carlo Simulations of Semi-Flexible Polymers
2005
We present Monte Carlo simulations on the phase behavior of semiflexible macromolecules. For a single chain this question is of biophysical interest given the fact that long and stiff DNA chains are typically folded up into very tight compartments. So one can ask the question how the state diagram of a semiflexible chain differs from the coilglobule behavior of a flexible macromolecule. Another effect connected with rigidity of the chains is their tendency to aggregate and form nematically ordered structures. As a consequence one has two competing phase transitions: a gas-liquid and an isotropic-nematic transition potentially giving rise to a complicated phase diagram.
Bifurcation of traveling waves in a Keller–Segel type free boundary model of cell motility
2018
We study a two-dimensional free boundary problem that models motility of eukaryotic cells on substrates. This problem consists of an elliptic equation describing the flow of cytoskeleton gel coupled with a convection-diffusion PDE for the density of myosin motors. The two key properties of this problem are (i) presence of the cross diffusion as in the classical Keller-Segel problem in chemotaxis and (ii) nonlinear nonlocal free boundary condition that involves curvature of the boundary. We establish the bifurcation of the traveling waves from a family of radially symmetric steady states. The traveling waves describe persistent motion without external cues or stimuli which is a signature of …
Field analysis of the magnetic systems for tubular linear reluctance motors
2005
We report a study of tubular linear reluctance motors (TLRMs) in various types of magnetic circuits. We carried out magnetic field analyses and calculated integral parameters of the field. We also determined static characteristics and electromagnetic parameters of the motor. We found good agreement between our calculations and tests of the motor with sinusoidal excitation.
Transition from plasma-driven to Kerr-driven laser filamentation.
2011
While filaments are generally interpreted as a dynamic balance between Kerr focusing and plasma defocusing, the role of the higher-order Kerr effect (HOKE) is actively debated as a potentially dominant defocusing contribution to filament stabilization. In a pump-probe experiment supported by numerical simulations, we demonstrate the transition between two distinct filamentation regimes at 800 nm. For long pulses (1.2 ps), the plasma substantially contributes to filamentation, while this contribution vanishes for short pulses (70 fs). These results confirm the occurrence, in adequate conditions, of filamentation driven by the HOKE rather than by plasma.
Force-clamp spectroscopy of reversible bond breakage.
2008
We consider reversible breaking of adhesion bonds or folding of proteins under the influence of a constant external force. We discuss the stochastic properties of the unbinding/rebinding events and analyze their mean number and their variance in the framework of simple two-state models. In the calculations, we exploit the analogy to single molecule fluorescence and particularly between unbinding/rebinding and photon emission events. Environmental fluctuation models are used to describe deviations from Markovian behavior. The second moment of the event-number distribution is found to be very sensitive to possible exchange processes and can thus be used to identify temporal fluctuations of th…
Effect of the Converging Pipe on the Performance of a Lucid Spherical Rotor
2018
Lucid spherical rotor is a cross-flow rotor developed to be installed within a pipeline. The purpose of installing this type of rotor is to collect excess energy available in gravity-fed water pipelines. In order to enhance the efficiency of the rotor which is installed in a channel, this paper aims to study the performance of Lucid spherical rotor with converging pipe. Numerical investigations were carried out to analyze the effect of the converging pipe on the performance of the rotor. Numerical simulations have been carried out using the unsteady Reynolds-averaged Navier–Stokes equations in conjunction with the realizable $$k-{\varepsilon }$$ turbulence model. The validation of the numer…
EnCurv: Simple Technique of Maintaining Global Membrane Curvature in Molecular Dynamics Simulations.
2021
The EnCurv method for maintaining membrane curvature in molecular dynamics simulations is introduced. The method allows maintaining any desired curvature in a sector of lipid membrane bent in a single plane without adding any unphysical interactions into the system and without restrictions on lateral and transversal lipid diffusion and distribution. The current implementation is limited to the membranes curved in a single plane but generalization to arbitrary curvature and membrane topology is possible. The method is simple, easy to implement, and scales linearly with the system size. EnCurv is agnostic to the force field, simulation parameters, and membrane composition. The proof of princi…
Ballistic phonon transport in dielectric membranes
2006
We have calculated the ballistic phononic heat transport in dielectric membranes as a function of radiator temperature and membrane thickness. The phonon modes of such membranes are known as Lamb-modes from elasticity theory. The striking result is that, for a fixed temperature, the radiated power first decreases with decreasing membrane thickness, but then develops a minimum when the transition to two dimensionality is reached. Further decrease of the membrane thickness in the 2D limit leads to increasing radiated power.
Membrane-mediated Protein-protein Interaction: A Monte Carlo Study
2012
We investigate membrane-mediated interactions between transmembrane proteins using coarse-grained models. We compare the effective potential of mean force (PMF) between two proteins, which are always aligned parallel to the z-axis of the simulation box, with those PMFs obtained for proteins with fluctuating orientations. The PMFs are dominated by an oscillatory packing-driven contribution and a smooth attractive hydrophobic mismatch contribution, which vanishes if the hydrophobic length of the protein matches the thickness of the membrane. If protein orientations are allowed to fluctuate, the oscillations are greatly reduced compared to proteins with fixed orientation. Furthermore, the hydr…