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Andrea J. Liu

Publications and source records attributed to Andrea J. Liu.

At least 109 records · Page 6Linked to original sources
arXiv2010

Electrostatic cluster formation in lipid monolayers

We study phase separation in mixed monolayers of neutral and highly negatively charged lipids, induced by the addition of divalent positively charged counterions. We find good agreement between experiments on mixtures of pip2 and sopc and simulations of a simplified model in which only the essential electrostatic interactions are retained. Thus, our results support an interpretation of pip2 clustering as governed primarily by electrostatic interactions, in which divalent ions such as calcium mediate an effective attraction between like-charged lipids. Surprisingly, the mediated attractions are strong enough to give nearly complete phase separation, so that clusters can even form when the overall concentration of pip2 is low, as is the case in the cell membrane.

cond-mat.soft↗
arXiv2009

Elasticity and Response in Nearly Isostatic Periodic Lattices

The square and kagome lattices with nearest neighbor springs of spring constant $k$ are isostatic with a number of zero-frequency modes that scale with their perimeter. We analytically study the approach to this isostatic limit as the spring constant $k'$ for next-nearest-neighbor bonds vanishes. We identify a characteristic frequency $ω^* \sim \sqrt{k'}$ and length $l^* \sim \sqrt{k/k'}$ for both lattices. The shear modulus $C_{44}= k'$ of the square lattice vanishes with $k'$, but that for the kagome lattice does not.

cond-mat.soft↗
arXiv2009

Equivalence of glass transition and colloidal glass transition in the hard-sphere limit

We show that the slowing of the dynamics in simulations of several model glass-forming liquids is equivalent to the hard-sphere glass transition in the low-pressure limit. In this limit, we find universal behavior of the relaxation time by collapsing molecular-dynamics data for all systems studied onto a single curve as a function of $T/p$, the ratio of the temperature to the pressure. At higher pressures, there are deviations from this universal behavior that depend on the inter-particle potential, implying that additional physical processes must enter into the dynamics of glass-formation.

cond-mat.soft↗
arXiv2009

Anharmonicity and quasi-localization of the excess low-frequency vibrations in jammed solids

We compare the harmonic and anharmonic properties of the vibrational modes in 3-dimensional jammed packings of frictionless spheres interacting via repulsive, finite range potentials. A crossover frequency is apparent in the density of states, the diffusivity and the participation ratio of the modes. At this frequency, which shifts to zero at the jamming threshold, the vibrational modes have a very small participation ratio implying that the modes are quasi-localized. The most anharmonic modes occur at low frequency which is opposite to what is normally found in crystals. The lowest frequency modes have the strongest response to the pressure and the lowest energy barriers to mechanical failure.

cond-mat.soft↗
arXiv2009

Heat transport in model jammed solids

We calculate numerically the normal modes of vibrations in 3D jammed packings of soft spheres as a function of the packing fraction and obtain the energy diffusivity, a spectral measure of transport that controls sound propagation and thermal conductivity. The crossover frequency between weak and strong phonon scattering is controlled by the coordination and shifts to zero as the system is decompressed towards the critical packing fraction at which rigidity is lost. Below the crossover, the diffusivity displays a power-law divergence with inverse frequency, which suggests that the vibrational modes are primarily transverse waves, weakly scattered by disorder. Above it, a large number of modes appear whose diffusivity plateaus at a nearly constant value independent of the inter-particle potential, before dropping to zero above the Anderson localization frequency. The thermal conductivity of a marginally jammed solid just above the rigidity threshold is calculated and related to the one measured experimentally at room temperature for most glasses.

cond-mat.dis-nn↗
arXiv2008

Energy transport in jammed sphere packings

We calculate the normal modes of vibration in jammed sphere packings to obtain the energy diffusivity, a spectral measure of transport. At the boson peak frequency, we find an Ioffe-Regel crossover from a diffusivity that drops rapidly with frequency to one that is nearly frequency-independent. This crossover frequency shifts to zero as the system is decompressed towards the jamming transition, providing unambiguous evidence of a regime in frequency of nearly constant diffusivity. Such a regime, postulated to exist in glasses to explain the temperature dependence of the thermal conductivity, therefore appears to arise from properties of the jamming transition.

cond-mat.soft↗
arXiv2008

New Proposed Mechanism of Actin-Polymerization-Driven Motility

We present the first numerical simulation of actin-driven propulsion by elastic filaments. Specifically, we use a Brownian dynamics formulation of the dendritic nucleation model of actin-driven propulsion. We show that the model leads to a self-assembled network that exerts forces on a disk and pushes it with an average speed. This simulation approach is the first to observe a speed that varies non-monotonically with the concentration of branching proteins (Arp2/3), capping protein and depolymerization rate (ADF), in accord with experimental observations. Our results suggest a new interpretation of the origin of motility that can be tested readily by experiment.

q-bio.CB↗
arXiv2008

Normal Modes in Model Jammed Systems in Three Dimensions

Vibrational spectra and normal modes of mechanically stable particle packings in three dimensions are analyzed over a range of compressions, from near the jamming transition, where the packings lose their rigidity, to far above it. At high frequency, the normal modes are localized at all compressions. At low frequency, the nature of the modes depends somewhat on compression. At large compressions, far from the transition, the lowest-frequency normal modes have some plane-wave character, though less than one would expect for a crystalline or isotropic solid. At low compressions near the jamming transition, the lowest-frequency modes are neither plane-wave-like nor localized. We characterize these differences, highlighting the unusual dispersion behavior that emerges for marginally jammed solids.

cond-mat.stat-mech↗
arXiv2007

Activated dynamics and effective temperature in a steady state sheared glass

We conduct nonequilibrium molecular dynamics simulations to measure the shear stress, the average inherent structure energy, and the effective temperature $T_{eff}$ of a sheared model glass as a function of bath temperature $T$ and shear strain rate. For $T$ above the glass transition temperature $T_0$, the rheology approaches a Newtonian limit and $T_{eff}$ approaches $T$ as the strain rate approaches zero, while for $T<T_0$, the shear stress approaches a yield stress and $T_{eff}$ approaches a limiting value near $T_0$. In the shear-dominated regime at high $T$, high strain rate or at low $T$, we find that the shear stress and the average inherent structure energy each collapse onto a single curve as a function of $T_{eff}$. This indicates that $T_{eff}$ is controlling behavior in this regime.

cond-mat.soft↗
arXiv2007

Why is Random Close Packing Reproducible?

We link the thermodynamics of colloidal suspensions to the statistics of regular and random packings. Random close packing has defied a rigorous definition yet, in three dimensions, there is near universal agreement on the volume fraction at which it occurs. We conjecture that the common value of phi_rcp, approximately 0.64, arises from a divergence in the rate at which accessible states disappear. We relate this rate to the equation of state for a hard sphere fluid on a metastable, non-crystalline branch.

cond-mat.stat-mech↗
arXiv2007

Branching, Capping, and Severing in Dynamic Actin Structures

Branched actin networks at the leading edge of a crawling cell evolve via protein-regulated processes such as polymerization, depolymerization, capping, branching, and severing. A formulation of these processes is presented and analyzed to study steady-state network morphology. In bulk, we identify several scaling regimes in severing and branching protein concentrations and find that the coupling between severing and branching is optimally exploited for conditions {\it in vivo}. Near the leading edge, we find qualitative agreement with the {\it in vivo} morphology.

cond-mat.soft↗
arXiv2006

Excess Vibrational Modes and the Boson Peak in Model Glasses

The excess low-frequency normal modes for two widely-used models of glasses were studied at zero temperature. The onset frequencies for the anomalous modes for both systems agree well with predictions of a variational argument, which is based on analyzing the vibrational energy originating from the excess contacts per particle over the minimum number needed for mechanical stability. Even though both glasses studied have a high coordination number, most of the additional contacts can be considered to be weak.

cond-mat.soft↗
arXiv2006

Structural signatures of the unjamming transition at zero temperature

We study the pair correlation function $g(r)$ for zero-temperature, disordered, soft-sphere packings just above the onset of jamming. We find distinct signatures of the transition in both the first and split second peaks of this function. As the transition is approached from the jammed side (at higher packing fraction) the first peak diverges and narrows on the small-$r$ side to a delta-function. On the high-$r$ side of this peak, $g(r)$ decays as a power-law. In the split second peak, the two subpeaks are both singular at the transition, with power-law behavior on their low-$r$ sides and step-function drop-offs on their high-$r$ sides. These singularities at the transition are reminiscent of empirical criteria that have previously been used to distinguish glassy structures from liquid ones.

cond-mat.stat-mech↗
arXiv2005

Structural Polymorphism of the Cytoskeleton: A Model of Linker-Assisted Filament Aggregation

The phase behavior of charged rods in the presence of inter-rod linkers is studied theoretically as a model for the equilibrium behavior underlying the organization of actin filaments by linker proteins in the cytoskeleton. The presence of linkers in the solution modifies the effective inter-rod interaction and can lead to inter-filament attraction. Depending on the system's composition and physical properties such as linker binding energies, filaments will either orient perpendicular or parallel to each other, leading to network-like or bundled structures. We show that such a system can have one of three generic phase diagrams, one dominated by bundles, another by networks, and the third containing both bundle and network-like phases. The first two diagrams can be found over a wide range of interaction energies, while the third occurs only for a narrow range. These results provide theoretical understanding of the classification of linker proteins as bundling proteins or crosslinking proteins. In addition, they suggest possible mechanisms by which the cell may control cytoskeletal morphology.

cond-mat.soft↗
arXiv2003

Effect of Mono- and Multivalent Salts on Angle-dependent Attractions between Charged Rods

Using molecular dynamics simulations we examine the effective interactions between two like-charged rods as a function of angle and separation. In particular, we determine how the competing electrostatic repulsions and multivalent-ion-induced attractions depend upon concentrations of simple and multivalent salt. We find that with increasing multivalent salt the stable configuration of two rods evolves from isolated rods to aggregated perpendicular rods to aggregated parallel rods; at sufficiently high concentration, additional multivalent salt reduces the attraction. Monovalent salt enhances the attraction near the onset of aggregation, and reduces it at higher concentration of multivalent salt.

cond-mat.soft↗
arXiv2001

Effective Temperatures of a Driven System Near Jamming

Fluctuations in a model of a sheared, zero-temperature foam are studied numerically. Five different quantities that reduce to the true temperature in an equilibrium thermal system are calculated. All five have the same shear-rate dependence, and three have the same value. Near the onset of jamming, the relaxation time is the same function of these three temperatures in the sheared system as of the true temperature in an unsheared system. These results imply that statistical mechanics is useful for the system and provide strong support for the concept of jamming.

cond-mat.soft↗
arXiv2000

Force distributions near the jamming and glass transitions

We calculate the distribution of interparticle normal forces $P(F)$ near the glass and jamming transitions in model supercooled liquids and foams, respectively. $P(F)$ develops a peak that appears near the glass or jamming transitions, whose height increases with decreasing temperature, decreasing shear stress and increasing packing density. A similar shape of $P(F)$ was observed in experiments on static granular packings. We propose that the appearance of this peak signals the development of a yield stress. The sensitivity of the peak to temperature, shear stress and density lends credence to the recently proposed generalized jamming phase diagram.

cond-mat.soft↗