arXiv subjects

Young C. Kim

Publications and source records attributed to Young C. Kim.

15 recordsLinked to original sources

arXiv2013

Crowding induced entropy-enthalpy compensation in protein association equilibria

A statistical mechanical theory is presented to predict the effects of macromolecular crowding on protein association equilibria, accounting for both excluded volume and attractive interactions between proteins and crowding molecules. Predicted binding free energies are in excellent agreement with simulation data over a wide range of crowder sizes and packing fraction. It is shown that attractive interactions between proteins and crowding agents counteract the stabilizing effects of excluded volume interactions. A critical attraction strength, for which there is no net effect of crowding, is almost independent of the crowder packing fraction.

cond-mat.soft↗

arXiv2005

Universality of Ionic Criticality: Size- and Charge-Asymmetric Electrolytes

Grand canonical simulations designed to resolve critical universality classes are reported for $z$:1 hard-core electrolyte models with diameter ratios $λ{=} a_+/a_- {\lesssim} 6$. For $z {=} 1$ Ising-type behavior prevails. Unbiased estimates of $T_c(λ)$ are within 1% of previous (biased) estimates but the critical densities are $\sim $5 % lower. Ising character is also established for the 2:1 and 3:1 equisized models, along with critical amplitudes and improved $T_c$ estimates. For $z {=} 3$, however, strong finite-size effects reduce the confidence level although classical and O$(n {\geq} 3)$ criticality are excluded.

cond-mat.soft↗

arXiv2005

Singular Coexistence-curve Diameters: Experiments and Simulations

Precise calculations of the coexistence-curve diameters of a hard-core square-we ll (HCSW) fluid and the restricted primitive model (RPM) electrolyte exhibit mar ked deviations from rectilinear behavior. The HCSW diameter displays a $|t|^{1- alpha}$ singularity that sets in sharply for $|t|\equiv |T-T_c|/T_c\lesssim 10^{-3}$; this compares favorably with extensive data for ${SF}_6$, also reflec ted in C$_2$H$_6$, N$_2$, etc. By contrast, the curvature of the RPM diameter va ries slowly over a wide range $|t|\lesssim 0.1$; this behavior mirrors observati ons for liquid alkali metals, specifically Rb and Cs. Amplitudes for the leading singular terms can be estimated numerically but their values cannot be taken li terally.

cond-mat.stat-mech↗

arXiv2005

Screening in Ionic Systems: Simulations for the Lebowitz Length

Simulations of the Lebowitz length, $ξ_{\text{L}}(T,ρ)$, are reported for t he restricted primitive model hard-core (diameter $a$) 1:1 electrolyte for densi ties $ρ\lesssim 4ρ_c$ and $T_c \lesssim T \lesssim 40T_c$. Finite-size eff ects are elucidated for the charge fluctuations in various subdomains that serve to evaluate $ξ_{\text{L}}$. On extrapolation to the bulk limit for $T\gtrsim 10T_c$ the low-density expansions (Bekiranov and Fisher, 1998) are seen to fail badly when $ρ> {1/10}ρ_c$ (with $ρ_c a^3 \simeq 0.08$). At highe r densities $ξ_{\text{L}}$ rises above the Debye length, $ξ_{\text{D}} \prop to \sqrt{T/ρ}$, by 10-30% (upto $ρ\simeq 1.3ρ_c$); the variation is portrayed fairly well by generalized Debye-Hückel theory (Lee and Fisher, 19 96). On approaching criticality at fixed $ρ$ or fixed $T$, $ξ_{\text{L}}(T, ρ)$ remains finite with $ξ_{\text{L}}^c \simeq 0.30 a \simeq 1.3 ξ_{\text {D}}^c$ but displays a weak entropy-like singularity.

cond-mat.soft↗

arXiv2005

Vectorial Loading of Processive Motor Proteins: Implementing a Landscape Picture

Individual processive molecular motors, of which conventional kinesin is the most studied quantitatively, move along polar molecular tracks and, by exerting a force ${\bm F} = (F_x,F_y,F_z)$ on a tether, drag cellular cargoes, {\em in vivo}, or spherical beads, {\em in vitro}, taking up to hundreds of nanometer-scale steps. From observations of velocities and the dispersion of displacements with time, under measured forces and controlled fuel supply (typically ATP), one may hope to obtain insight into the molecular motions undergone in the individual steps. In the simplest situation, the load force ${\bm F}$ may be regarded as a scalar resisting force, $F_x < 0$, acting parallel to the track: however, experiments, originally by Gittes {\em et al.} (1996), have imposed perpendicular (or vertical) loads, $F_z > 0$, while more recently Block and coworkers (2002, 2003) and Carter and Cross (2005) have studied {\em assisting} (or reverse) loads, $F_x > 0$, and also sideways (or transverse) loads $F_y \neq 0$.

cond-mat.stat-mech↗

arXiv2005

Yang-Yang Anomalies and Coexistence Diameters: Simulation of Asymmetric Fluids

A general method for estimating the Yang-Yang ratio, ${\cal R}_μ$, and the coexistence-curve diameter of a model fluid via Monte Carlo simulations is presented on the basis of data for a hard-core square-well (HCSW) fluid and the restricted primitive model (RPM) electrolyte. The isothermal minima of $Q_{L}\equiv< m^{2}>^{2}_{L}/< m^{4}>_{L}$ are evaluated at $T_{c}$ in an $L\times L\times L$ box where $m = ρ- <ρ>_{L}$ is the density fluctuation. The ``complete'' finite-size scaling theory for the $Q_{\scriptsize min}^{\pm}(T_{c};L)$ incorporates pressure mixing in the scaling fields, thereby allowing for a Yang-Yang anomaly.

cond-mat.stat-mech↗

arXiv2005

Convergence of Fine-lattice Discretization for Near-critical Fluids

In simulating continuum model fluids that undergo phase separation and criticality, significant gains in computational efficiency may be had by confining the particles to the sites of a lattice of sufficiently fine spacing, $a_{0}$ (relative to the particle size, say $a$). But a cardinal question, investigated here, then arises, namely: How does the choice of the lattice discretization parameter, $ζ\equiv a/a_{0}$, affect the values of interesting parameters, specifically, critical temperature and density, $T_{\scriptsize c}$ and $ρ_{\scriptsize c}$? Indeed, for small $ζ(\lesssim 4 $-$ 8)$ the underlying lattice can strongly influence the thermodynamic properties. A heuristic argument, essentially exact in $d=1$ and $d=2$ dimensions, indicates that for models with hard-core potentials, both $T_{\scriptsize c}(ζ)$ and $ρ_{\scriptsize c}(ζ)$ should converge to their continuum limits as $1/ζ^{(d+1)/2}$ for $d\leq 3$ when $ζ\to\infty$; but the behavior of the error is highly erratic for $d\geq 2$. For smoother interaction potentials, the convergence is faster. Exact results for $d=1$ models of van der Waals character confirm this; however, an optimal choice of $ζ$ can improve the rate of convergence by a factor $1/ζ$. For $d\geq 2$ models, the convergence of the {\em second virial coefficients} to their continuum limits likewise exhibit erratic behavior which is seen to transfer similarly to $T_{\scriptsize c}$ and $ρ_{\scriptsize c}$; but this can be used in various ways to enhance convergence and improve extrapolation to $ζ= \infty$ as is illustrated using data for the restricted primitive model electrolyte.

cond-mat.stat-mech↗

arXiv2004

Fluid Coexistence close to Criticality: Scaling Algorithms for Precise Simulation

A novel algorithm is presented that yields precise estimates of coexisting liquid and gas densities, $ρ^{\pm}(T)$, from grand canonical Monte Carlo simulations of model fluids near criticality. The algorithm utilizes data for the isothermal minima of the moment ratio $Q_{L}(T;<ρ>_{L})$ $\equiv< m^{2}>_{L}^{2}/< m^{4}>_{L}$ in $L$$ \times$$ ...$$ \times$$ L$ boxes, where $m=ρ-<ρ>_{L}$. When $L$$ \to$$ \infty$ the minima, $Q_{\scriptsize m}^{\pm}(T;L)$, tend to zero while their locations, $ρ_{\scriptsize m}^{\pm}(T;L)$, approach $ρ^{+}(T)$ and $ρ^{-}(T)$. Finite-size scaling relates the ratio {\boldmath $\mathcal Y$}$ = $$(ρ_{\scriptsize m}^{+}-ρ_{\scriptsize m}^{-})/Δρ_{\infty}(T)$ {\em universally} to ${1/2}(Q_{\scriptsize m}^{+}+Q_{\scriptsize m}^{-})$, where $Δρ_{\infty}$$ = $$ρ^{+}(T)-ρ^{-}(T)$ is the desired width of the coexistence curve. Utilizing the exact limiting $(L$$ \to $$\infty)$ form, the corresponding scaling function can be generated in recursive steps by fitting overlapping data for three or more box sizes, $L_{1}$, $L_{2}$, $...$, $L_{n}$. Starting at a $T_{0}$ sufficiently far below $T_{\scriptsize c}$ and suitably choosing intervals $ΔT_{j}$$ = $$T_{j+1}-T_{j}$$ > $0 yields $Δρ_{\infty}(T_{j})$ and precisely locates $T_{\scriptsize c}$.

cond-mat.stat-mech↗

arXiv2004

Discretization Dependence of Criticality in Model Fluids: a Hard-core Electrolyte

Grand canonical simulations at various levels, $ζ=5$-20, of fine- lattice discretization are reported for the near-critical 1:1 hard-core electrolyte or RPM. With the aid of finite-size scaling analyses it is shown convincingly that, contrary to recent suggestions, the universal critical behavior is independent of $ζ$ $(\grtsim 4)$; thus the continuum $(ζ\to\infty)$ RPM exhibits Ising-type (as against classical, SAW, XY, etc.) criticality. A general consideration of lattice discretization provides effective extrapolation of the {\em intrinsically} erratic $ζ$-dependence, yielding $(\Tc^ {\ast},\rhoc^{\ast})\simeq (0.0493_{3},0.075)$ for the $ζ=\infty$ RPM.

cond-mat.stat-mech↗

arXiv2003

Fluid Critical Points from Simulations: the Bruce-Wilding method and Yang-Yang anomalies

A critique is presented of the frequently used Bruce-Wilding (BW) mixed-field scaling method for estimating the critical points of nonsymmetric model fluids from grand canonical simulation data. An explicit, systematic technique for implementing this method is set out thereby revealing clearly a fortunate, close cancelation of contributions from the leading correction- to-scaling and thermal scaling functions that makes the method effective for Ising-type systems but which lacks a general theoretical basis. Pressure mixing is considered in this work which modifies the leading behavior of the critical density estimator while the critical temperature estimator maintains the leading behavior asserted by BW.

cond-mat.stat-mech↗

arXiv2003

Precise Simulation of Near-critical Fluid Coexistence

We present a novel method to derive liquid-gas coexisting densities, $ρ^{\pm}(T)$, from grand canonical simulations (without knowledge of $\Tc$ or criticality class). The minima of $ Q_{L}\equiv< m^{2} >_{L}^{2}/< m^{4}>_{L}$ in an $L$$\times$$L \times$$L$ box with $m = ρ- <ρ>_{L}$ are used to generate recursively an unbiased universal finite-size scaling function. Monte Carlo data for a hard-core square-well fluid and for the restricted primitive model electrolyte yield $ρ^{\pm}$ to $\pm 1$-2% of $\rhoc$ down to 1 part in $10^4$-$10^3$ of $\Tc$ (and confirm well Ising character). Pressure mixing in the scaling fields is unequivocally revealed and indicates Yang-Yang ratios $R_μ = -0.04_{4}$ and $0.2_{6}$ for the two models, respectively.

cond-mat.stat-mech↗

arXiv2003

Asymmetric Fluid Criticality II: Finite-Size Scaling for Simulations

The vapor-liquid critical behavior of intrinsically asymmetric fluids is studied in finite systems of linear dimensions, $L$, focusing on periodic boundary conditions, as appropriate for simulations. The recently propounded ``complete'' thermodynamic $(L\to\infty)$ scaling theory incorporating pressure mixing in the scaling fields as well as corrections to scaling ${[arXiv:cond-mat/0212145]}$, is extended to finite $L$, initially in a grand canonical representation. The theory allows for a Yang-Yang anomaly in which, when $L\to\infty$, the second temperature derivative, $(d^{2}μ_σ/dT^{2})$, of the chemical potential along the phase boundary, $μ_σ(T)$, diverges when $T\to\Tc -$. The finite-size behavior of various special {\em critical loci} in the temperature-density or $(T,ρ)$ plane, in particular, the $k$-inflection susceptibility loci and the $Q$-maximal loci -- derived from $Q_{L}(T,<ρ>_{L}) \equiv < m^{2}>^{2}_{L}/< m^{4}>_{L}$ where $m \equiv ρ- <ρ>_{L}$ -- is carefully elucidated and shown to be of value in estimating $\Tc$ and $\rhoc$. Concrete illustrations are presented for the hard-core square-well fluid and for the restricted primitive model electrolyte including an estimate of the correlation exponent $ν$ that confirms Ising-type character. The treatment is extended to the canonical representation where further complications appear.

cond-mat.stat-mech↗

arXiv2002

Asymmetric Fluid Criticality I: Scaling with Pressure Mixing

The thermodynamic behavior of a fluid near a vapor-liquid and, hence, asymmetric critical point is discussed within a general ``complete'' scaling theory incorporating pressure mixing in the nonlinear scaling fields as well as corrections to scaling. This theory allows for a Yang-Yang anomaly in which μ_σ^{\prime\prime}(T), the second temperature derivative of the chemical potential along the phase boundary, diverges like the specific heat when T\to T_{\scriptsize c}; it also generates a leading singular term, |t|^{2β}, in the coexistence curve diameter, where t\equiv (T-T_{\scriptsize c}) /T_{\scriptsize c}. The behavior of various special loci, such as the critical isochore, the critical isotherm, the k-inflection loci, on which χ^{(k)}\equiv χ(ρ,T)/ρ^{k} (with χ= ρ^{2} k_{\scriptsize B}TK_{T}) and C_{V}^{(k)}\equiv C_{V}(ρ,T)/ρ^{k} are maximal at fixed T, is carefully elucidated. These results are useful for analyzing simulations and experiments, since particular, nonuniversal values of k specify loci that approach the critical density most rapidly and reflect the pressure-mixing coefficient. Concrete illustrations are presented for the hard-core square-well fluid and for the restricted primitive model electrolyte. For comparison, a discussion of the classical (or Landau) theory is presented briefly and various interesting loci are determined explicitly and illustrated quantitatively for a van der Waals fluid.

cond-mat.stat-mech↗

arXiv2002

Crossover critical behavior in the three-dimensional Ising model

The character of critical behavior in physical systems depends on the range of interactions. In the limit of infinite range of the interactions, systems will exhibit mean-field critical behavior, i.e., critical behavior not affected by fluctuations of the order parameter. If the interaction range is finite, the critical behavior asymptotically close to the critical point is determined by fluctuations and the actual critical behavior depends on the particular universality class. A variety of systems, including fluids and anisotropic ferromagnets, belongs to the three-dimensional Ising universality class. Recent numerical studies of Ising models with different interaction ranges have revealed a spectacular crossover between the asymptotic fluctuation-induced critical behavior and mean-field-type critical behavior. In this work, we compare these numerical results with a crossover Landau model based on renormalization-group matching. For this purpose we consider an application of the crossover Landau model to the three-dimensional Ising model without fitting to any adjustable parameters. The crossover behavior of the critical susceptibility and of the order parameter is analyzed over a broad range (ten orders) of the scaled distance to the critical temperature. The dependence of the coupling constant on the interaction range, governing the crossover critical behavior, is discussed

cond-mat.stat-mech↗

arXiv2001

The Isothermal Binodal Curves Near a Critical Endpoint

Thermodynamics in the vicinity of a critical endpoint with nonclassical exponents $α$, $β$, $γ$, $δ$, $...$ is analyzed in terms of density variables (mole fractions, magnetizations, etc.). The shapes of the isothermal binodals or two-phase coexistence curves are found at andnear the endpoint for symmetric and nonsymmetric situations. The spectator- (or noncritical)-phase binodal at $T=T_{e}$ is characterized by an exponent $(δ+1)/δ$ $(\simeq 1.21)$ with leading corrections of relative order $1/δ$ $(\simeq 0.21)$, $θ_{4}/βδ$ $(\simeq 0.34)$ and $1 -(βδ)^{-1}$$(\simeq 0.36)$; in contrast to classical (van der Waals, mean field, $...$) theory, the critical endpoint binodal is singular with leading exponent $(1-α)/β$ $(\simeq 2.73)$ and corrections which are elucidated; the remaining, $λ$-line binodals also display the `renormalized exponent,' $(1-α)/β$ butwith more singular corrections. (The numerical values quoted here pertain to $(d=3)$-dimensional-fluid or Ising-type systems.)

cond-mat↗