Biomedical subjects

Andrea J Liu

Publications and source records attributed to Andrea J Liu.

10 recordsLinked to original sources

PubMed2006

Polyamine-induced bundling of F-actin.

To better understand the mechanism of actin filament (F-actin) bundling by polyamines, we have measured the onset of bundling as a function of polyamine concentration. Samples were centrifuged at low speeds to separate bundles from unbundled actin, and the relative amounts of actin in the pellet and supernatant were determined via gel electrophoresis, yielding a description of the bundling transition as a function of actin and polyamine concentrations. These experiments were carried out for two different polyamines, spermine (tetravalent) and spermidine (trivalent). We found that the threshold concentration of polyamine needed to bundle actin is independent of both actin concentration and Mg2+ concentration over a wide range in Mg2+ concentration. We also find that spermine in F-actin bundles is essentially invisible in solution-phase proton NMR, suggesting that it is bound so tightly to F-actin that it is immobilized.

Actin Cytoskeleton↗

PubMed2006

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.

Journal Article↗

PubMed2005

Vibrations and diverging length scales near the unjamming transition.

We numerically study the vibrations of jammed packings of particles interacting with finite-range, repulsive potentials at zero temperature. As the packing fraction phi is lowered towards the onset of unjamming at phi(c), the density of vibrational states approaches a nonzero value in the limit of zero frequency. For phi >phi(c), there is a crossover frequency, omega* below which the density of states drops towards zero. This crossover frequency obeys power-law scaling with phi-phi(c). Characteristic length scales, determined from the dominant wave vector contributing to the eigenmode at omega*, diverge as power laws at the unjamming transition.

Journal Article↗

PubMed2005

Structural polymorphism of the cytoskeleton: a model of linker-assisted filament aggregation.

The phase behavior of charged rods in the presence of interrod 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 interrod interaction and can lead to interfilament attraction. Depending on the composition and physical properties of the system, such as linker-binding energies, filaments will orient either 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, whereas the third diagram 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.

Actins↗

PubMed2004

Effective temperatures in driven systems: static versus time-dependent relations.

Using simulations of glassy systems under steady-state shear, we compare effective temperatures obtained from static linear response with those from time-dependent fluctuation-dissipation relations. Although these two definitions are not expected to agree, we show that they yield the same answer over two and a half decades of effective temperature. This suggests that a more complete conceptual framework is necessary for effective temperatures in steady-state driven systems.

Journal Article↗

PubMed2004

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 salts. 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 a higher concentration of multivalent salt.

Journal Article↗

PubMed2003

Jamming at zero temperature and zero applied stress: the epitome of disorder.

We have studied how two- and three-dimensional systems made up of particles interacting with finite range, repulsive potentials jam (i.e., develop a yield stress in a disordered state) at zero temperature and zero applied stress. At low packing fractions phi, the system is not jammed and each particle can move without impediment from its neighbors. For each configuration, there is a unique jamming threshold phi(c) at which particles can no longer avoid each other, and the bulk and shear moduli simultaneously become nonzero. The distribution of phi(c) values becomes narrower as the system size increases, so that essentially all configurations jam at the same packing fraction in the thermodynamic limit. This packing fraction corresponds to the previously measured value for random close packing. In fact, our results provide a well-defined meaning for "random close packing" in terms of the fraction of all phase space with inherent structures that jam. The jamming threshold, point J, occurring at zero temperature and applied stress and at the random-close-packing density, has properties reminiscent of an ordinary critical point. As point J is approached from higher packing fractions, power-law scaling is found for the divergence of the first peak in the pair correlation function and in the vanishing of the pressure, shear modulus, and excess number of overlapping neighbors. Moreover, near point J, certain quantities no longer self-average, suggesting the existence of a length scale that diverges at J. However, point J also differs from an ordinary critical point: the scaling exponents do not depend on dimension but do depend on the interparticle potential. Finally, as point J is approached from high packing fractions, the density of vibrational states develops a large excess of low-frequency modes. Indeed, at point J, the density of states is a constant all the way down to zero frequency. All of these results suggest that point J is a point of maximal disorder and may control behavior in its vicinity-perhaps even at the glass transition.

Journal Article↗

PubMed2003

Velocity fluctuations in a steadily sheared model foam.

Numerical simulations are conducted to calculate velocity fluctuations in a simple two-dimensional model of foam under steady shear. The width of the velocity distribution increases sublinearly with the shear rate, indicating that velocity fluctuations are large compared to the average flow at low shear rates (stick-slip flow) and small compared to the average flow at large shear rates. Several quantities reveal a crossover in behavior at a characteristic strain rate gamma(x), given by the yield strain divided by the duration of a bubble rearrangement event. For strain rates above gamma(x), the velocity correlations decay exponentially in space and time, and the velocity distribution is a Gaussian. For strain rates below gamma(x), the velocity correlations decay as stretched exponentials in space and time, and the velocity distribution is broader than a Gaussian.

Journal Article↗

PubMed2002

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 independently reduce to the true temperature in an equilibrium thermal system are calculated. One of the quantities is calculated up to an unknown coefficient. The other four quantities have the same value and all five have the same shear-rate dependence. These results imply that statistical mechanics is useful for the system even though it is far from thermal equilibrium.

Journal Article↗

PubMed2002

Random packings of frictionless particles.

We conduct numerical simulations of random packings of frictionless particles at T = 0. The packing fraction where the pressure becomes nonzero is the same as the jamming threshold, where the static shear modulus becomes nonzero. The distribution of threshold packing fractions narrows, and its peak approaches random close packing as the system size increases. For packing fractions within the peak, there is no self-averaging, leading to exponential decay of the interparticle force distribution.

Journal Article↗