arXiv subjects

Tom Chou

Publications and source records attributed to Tom Chou.

106 records · Page 6Linked to original sources

arXiv2002

A length-dynamic Tonks gas theory of histone isotherms

We find exact solutions to a new one-dimensional (1D) interacting particle theory and apply the results to the adsorption and wrapping of polymers (such as DNA) around protein particles (such as histones). Each adsorbed protein is represented by a Tonks gas particle. The length of each particle is a degree of freedom that represents the degree of DNA wrapping around each histone. Thermodynamic quantities are computed as functions of wrapping energy, adsorbed histone density, and bulk histone concentration (or chemical potential); their experimental signatures are also discussed. Histone density is found to undergo a two-stage adsorption process as a function of chemical potential, while the mean coverage by high affinity proteins exhibits a maximum as a function of the chemical potential. However, {\it fluctuations} in the coverage are concurrently maximal. Histone-histone correlation functions are also computed and exhibit rich two length scale behavior.

cond-mat.soft↗

arXiv2002

An interacting spin flip model for one-dimensional proton conduction

A discrete asymmetric exclusion process (ASEP) is developed to model proton conduction along one-dimensional water wires. Each lattice site represents a water molecule that can be in only one of three states; protonated, left-pointing, and right-pointing. Only a right(left)-pointing water can accept a proton from its left(right). Results of asymptotic mean field analysis and Monte-Carlo simulations for the three-species, open boundary exclusion model are presented and compared. The mean field results for the steady-state proton current suggest a number of regimes analogous to the low and maximal current phases found in the single species ASEP [B. Derrida, Physics Reports, {\bf 301}, 65-83, (1998)]. We find that the mean field results are accurate (compared with lattice Monte-Carlo simulations) only in the certain regimes. Refinements and extensions including more elaborate forces and pore defects are also discussed.

cond-mat.stat-mech↗

arXiv2001

Geometry-dependent electrostatics near contact lines

Long-ranged electrostatic interactions in electrolytes modify their contact angles on charged substrates in a scale and geometry dependent manner. For angles measured at scales smaller than the typical Debye screening length, the wetting geometry near the contact line must be explicitly considered. Using variational and asymptotic methods, we derive new transcendental equations for the contact angle that depend on the electrostatic potential only at the three phase contact line. Analytic expressions are found in certain limits and compared with predictions for contact angles measured with lower resolution. An estimate for electrostatic contributions to {\it line} tension is also given.

cond-mat.soft↗

arXiv2001

Surface-dependent Coagulation Enzymes: Flow Kinetics of Factor Xa Generation on Live Membranes

The initial surface reactions of the extrinsic coagulation pathway on live cell membranes were examined under flow conditions. Generation of fXa (activated coagulation factor X) was measured on spherical monolayers of epithelial cells with a total surface area of 41-47 cm$^{2}$ expressing TF(tissue factor) at $>25$ fmol/cm$^{2}$. Concentrations of reactants and product were monitored as a function of time with radiolabeled proteins and a chromogenic substrate at resolutions of 2-8 s. At physiological concentrations of fVIIa and fX, the reaction rate was $3.05 \pm 0.75$ fmol fXa/s/cm$^{2}$, independent of flux, and 10 times slower than that expected for collision-limited reactions. Rates were also independent of surface fVIIa concentrations within the range 0.6-25 fmol/cm$^{2}$. The transit time of fX activated on the reaction chamber was prolonged relative to transit times of nonreacting tracers or preformed fXa. Membrane reactions were modeled using a set of nonlinear kinetic equations and a lagged normal density curve to track the expected surface concentration of reactants for various hypothetical reaction mechanisms. The experimental results were theoretically predicted only when the models used a slow intermediate reaction step, consistent with surface diffusion. These results provide evidence that the transfer of substrate within the membrane is rate-limiting in the kinetic mechanisms leading to initiation of blood coagulation by the tissue factor pathway.

cond-mat.soft↗

arXiv2000

Statistical thermodynamics of membrane bending mediated protein-protein attraction

Integral membrane proteins deform the surrounding bilayer creating long-ranged forces that influence distant proteins. These forces can be attractive or repulsive, depending on the proteins' shape, height, contact angle with the bilayer, as well as the local membrane curvature. Although interaction energies are not pairwise additive, for sufficiently low protein density, thermodynamic properties depend only upon pair interactions. Here, we compute pair interaction potentials and entropic contributions to the two-dimensional osmotic pressure of a collection of noncircular proteins. In contrast to direct short-ranged interactions such as van der Waal's, hydrophobic, or electrostatic interactions, both local membrane Gaussian curvature and protein ellipticity can induce attractions between two proteins at distances of up to ten times their typical radii. For flat membranes, bending rigidities of $\sim 30k_{B}T$, and moderate ellipticities, we find thermally averaged attractive interactions of order $\sim 2k_{B}T$. These interactions may play an important role in the intermediate stages of protein aggregation.

cond-mat.stat-mech↗

arXiv2000

Capillary-gravity wave transport over spatially random drift

We derive transport equations for the propagation of water wave action in the presence of a static, spatially random surface drift. Using the Wigner distribution $\W(\x,\k,t)$ to represent the envelope of the wave amplitude at position $\x$ contained in waves with wavevector $\k$, we describe surface wave transport over static flows consisting of two length scales; one varying smoothly on the wavelength scale, the other varying on a scale comparable to the wavelength. The spatially rapidly varying but weak surface flows augment the characteristic equations with scattering terms that are explicit functions of the correlations of the random surface currents. These scattering terms depend parametrically on the magnitudes and directions of the smoothly varying drift and are shown to give rise to a Doppler coupled scattering mechanism. The Doppler interaction in the presence of slowly varying drift modifies the scattering processes and provides a mechanism for coupling long wavelengths with short wavelengths. Conservation of wave action (CWA), typically derived for slowly varying drift, is extended to systems with rapidly varying flow. At yet larger propagation distances, we derive from the transport equations, an equation for wave energy diffusion. The associated diffusion constant is also expressed in terms of the surface flow correlations. Our results provide a formal set of equations to analyse transport of surface wave action, intensity, energy, and wave scattering as a function of the slowly varying drifts and the correlation functions of the random, highly oscillatory surface flows.

physics.flu-dyn↗

arXiv1999

Entropy-driven pumping across zeolites and biological channels

When two binary solutions are separated by a permeable barrier, the individual species typically diffuse and mix, dissipating their chemical potential gradients. However, we use model lattice simulations to show that single-file molecular-sized channels (such biomembrane channels and zeolites) can exhibit diffusional pumping, where one type of particle uses its entropy of mixing to drive another up its chemical potential gradient. Quantitative analyses of rates and efficiencies of transport are plotted as functions of transmembrane potential, pore length, and particle-pore interactions. Our results qualitatively explain recent measurements of ``negative'' osmosis and suggest new, more systematic experiments, particularly in zeolite transport systems.

cond-mat.stat-mech↗

arXiv1998

Kinetics and thermodynamics across single-file pores: solute permeability and rectified osmosis

We study the effects of solute interactions on osmotic transport through pores. By extending single-file, single-species kinetic models to include entrance of solute into membrane pores, we model the statistical mechanics of competitive transport of two species across membrane pores. The results have direct applications to water transport across biomembrane pores and particle movement in zeolites, and can be extended to study ion channel transport. Reflection coefficients, the reduction of osmotic fluxes measured using different solutes, are computed in terms of the microscopic kinetic parameters. We find that a reduction in solvent flow due to solute-pore interactions can be modelled by a Langmuir adsorption isotherm. Osmosis experiments are discussed and proposed. Special cases and Onsager relations are presented in the Appendices.

cond-mat.mtrl-sci↗

arXiv1998

Kinetics of nanopore transport

A nonlinear kinetic exclusion model is used to study osmosis and pressure driven flows through nearly single file pores such as antibiotic channels, aquaporins, zeolites and nanotubules. Two possible maxima in the steady state flux as a function of pore-solvent affinity are found. For small driving forces, the linear macroscopic osmotic and hydraulic permeabilities $P_{os}$ and $L_{p}$, are defined in terms of microscopic kinetic parameters. The dependences of the flux on activation energies, pore length and radius, and driving forces are explored and Arrhenius temperature dependences derived. Reasonable values for the physical parameters used in the analyses yield transport rates consistent with experimental measurements. Experimental consequences and interpretations are examined, and a straightforward extension to osmosis through disordered pores is given.

cond-mat.soft↗

arXiv1997

Liquid Surface Wave Band Structure Instabilities

We study interfacial instabilities between two spatially periodically sheared ideal fluids. Bloch wavefunction decompositions of the surface deformation and fluid velocities result in a nonhermitian secular matrix with an associated band structure that yields both linear oscillating and nonoscillating instabilities, enhanced near Bragg planes corresponding to the periodicity determined by converging or diverging surface flows. The instabilities persist even when the dynamical effects of the upper fluid are neglected, in contrast to the uniform shear Kelvin-Helmholtz (KH) instability. Periodic flows can also couple with uniform shear and suppress standard KH instabilities.

cond-mat.soft↗

arXiv1997

How fast can fluids squeeze through micro-pores?

We use a one dimensional symmetric exclusion model to study pressure and osmosis driven flows through molecular-sized channels, such as biological membrane channels and zeolite pores. Analytic expressions are found for the steady-state flow which show rich nonlinear behavior. We find a maximum in the flow rates depending upon pore radius, pore energetics, reservoir temperature, and driving force. We also present exact mean-field results of transport through pores with internal defects. The interesting nonlinear dependences suggest numerous diagnostic experiments in biological and zeolitic systems which may reveal the features presented.

cond-mat.soft↗

arXiv1997

A Vorticity-Magnetic Field Dynamo Instability

We generalize the mean field magnetic dynamo to include local evolution of the mean vorticity in addition to the mean magnetic field. The coupled equations exhibit a general mean field dynamo instability that enables the transfer of turbulent energy to the magnetic field and vorticity on larger scales. The growth of the vorticity and magnetic field both require helical turbulence which can be supplied by an underlying global rotation. The dynamo coefficients are derived including the backreaction from the mean magnetic field to lowest order. We find that a mean vorticity field can actually seed exponential growth of mean magnetic field from only a small scale seed magnetic field, without the need for a seed mean magnetic field. The equations decouple when the fluctuating velocity and magnetic field cross-correlations vanish, resulting in the separate mean field magnetic and mean field vorticity dynamo equations.

astro-ph↗

arXiv1997

Band Structure of Periodically Surface-Scattered Water Waves

Bloch wavefunctions are used to derive dispersion relations for water wave propagation in the presence of an infinite array of periodically arranged surface scatterers. For one dimensional periodicity (stripes), band gaps for wavevectors in the direction of periodicity are found corresponding to multiple Bragg scattering. The dependence of these band gaps as a function of scatterer density, strength, and water depth is analyzed. We find in contrast to band gap behavior in electronic, photonic, and acoustic systems, these gaps can increase with excitation frequency $ω$. Thus, higher order Bragg scattering can play a dominant role in suppressing wave propagation. Furthermore, in one dimension, an additional constraint (in addition to single scatterer energy and momentum conservation) on the calculation of transmission $T$ and reflection $R$ coefficients of a finite number of scatterers is calculated from the exact dispersion relation of the infinite periodic system. This relationship may be useful in measurements where only phase or amplitude is easily measured. In simple two dimensional periodic geometries, we find no complete band gaps and offer semi-quantitative reasons for why this is so. The role of evanescent modes is discussed, and finally, equations for water wave band structure in the presence of a uniform flow are derived.

cond-mat↗

arXiv1996

Electrostatics of Lipid Bilayer Bending

The electrostatic contribution to spontaneous membrane curvature is calculated within Poisson-Boltzmann theory under a variety of assumptions and emphasizing parameters in the physiological range. Asymmetric surface charges, either fixed with respect to bilayer midplane area, or with respect to the lipid-water area both induce curvature but of opposite sign. Unequal screening layers on the two sides of a vesicle ({\it e.g.} multivalent cationic proteins on one side and monovalent salt on the other) also induces bending. For reasonable parameters, tubules formed by electrostatically induced bending can have radii in the 50-100nm range, often seen in many intracellular organelles. Thus membrane associated proteins may induce curvature and subsequent budding, without themselves being intrinsically curved. Furthermore, we derive the previously unexplored effects of respecting the strict conservation of charge within the interior of a vesicle. The electrostatic component to the bending modulus is small under most of our conditions, and is left as an experimental parameter. The large parameter space of conditions is surveyed in an array of graphs.

cond-mat↗

arXiv1996

Counter-rotating Accretion Disks

We consider accretion disks consisting of counter-rotating gaseous components with an intervening shear layer. Configurations of this type may arise from the accretion of newly supplied counter-rotating gas onto an existing co-rotating gas disk. For simplicity we consider the case where the gas well above the disk midplane is rotating with angular rate $+Ω$ and that well below has the same properties but is rotating with rate $-Ω$. Using the Shakura-Sunyaev alpha turbulence model, we find self-similar solutions where a thin (relative to the full disk thickness) equatorial layer accretes very rapidly, essentially at free-fall speed. As a result the accretion speed is much larger than it would be for an alpha disk rotating in one direction. Counter-rotating accretion disks may be a transient stage in the formation of counter-rotating galaxies and in the accretion of matter onto compact objects.

astro-ph↗

arXiv1995

A magnetic field diagnostic for sonoluminescence

This study is motivated by the extraordinary process of single bubble sonoluminescence (SBSL), where an acoustically driven spherical shock is thought to power the emitted radiation. We propose new experiments using an external magnetic field which can induce anisotropies in both the shock propagation and radiation pattern. The effects will depend on the temperature, conductivity, and size of the radiating region. Our predictions suggest that such a laboratory experiment could serve as an important diagnostic in placing bounds on these parameters and understanding the physics of sonoluminescence.

cond-mat↗