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Phillip L. Geissler

Publications and source records attributed to Phillip L. Geissler.

50 records · Page 3Linked to original sources
arXiv2009

The role of collective motion in examples of coarsening and self-assembly

The simplest prescription for building a patterned structure from its constituents is to add particles, one at a time, to an appropriate template. However, self-organizing molecular and colloidal systems in nature can evolve in much more hierarchical ways. Specifically, constituents (or clusters of constituents) may aggregate to form clusters (or clusters of clusters) that serve as building blocks for later stages of assembly. Here we evaluate the character and consequences of such collective motion in a set of prototypical assembly processes. We do so using computer simulations in which a system's capacity for hierarchical dynamics can be controlled systematically. By explicitly allowing or suppressing collective motion, we quantify its effects. We find that coarsening within a two dimensional attractive lattice gas (and an analogous off-lattice model in three dimensions) is naturally dominated by collective motion over a broad range of temperatures and densities. Under such circumstances, cluster mobility inhibits the development of uniform coexisting phases, especially when macroscopic segregation is strongly favored by thermodynamics. By contrast, the assembly of model viral capsids is not frustrated but is instead facilitated by collective moves, which promote the orderly binding of intermediates consisting of several monomers.

cond-mat.stat-mech↗
arXiv2009

The limited role of non-native contacts in folding pathways of a lattice protein

Models of protein energetics which neglect interactions between amino acids that are not adjacent in the native state, such as the Go model, encode or underlie many influential ideas on protein folding. Implicit in this simplification is a crucial assumption that has never been critically evaluated in a broad context: Detailed mechanisms of protein folding are not biased by non-native contacts, typically imagined as a consequence of sequence design and/or topology. Here we present, using computer simulations of a well-studied lattice heteropolymer model, the first systematic test of this oft-assumed correspondence over the statistically significant range of hundreds of thousands of amino acid sequences, and a concomitantly diverse set of folding pathways. Enabled by a novel means of fingerprinting folding trajectories, our study reveals a profound insensitivity of the order in which native contacts accumulate to the omission of non-native interactions. Contrary to conventional thinking, this robustness does not arise from topological restrictions and does not depend on folding rate. We find instead that the crucial factor in discriminating among topological pathways is the heterogeneity of native contact energies. Our results challenge conventional thinking on the relationship between sequence design and free energy landscapes for protein folding, and help justify the widespread use of Go-like models to scrutinize detailed folding mechanisms of real proteins.

q-bio.BM↗
arXiv2008

Stretching chimeric DNA: a test for the putative S-form

Double-stranded DNA `overstretches' at a pulling force of about 65 pN, increasing in length by a factor of 1.7. The nature of the overstretched state is unknown, despite its considerable importance for DNA's biological function and technological application. Overstretching is thought by some to be a force-induced denaturation, and by others to consist of a transition to an elongated, hybridized state called S-DNA. Within a statistical mechanical model we consider the effect upon overstretching of extreme sequence heterogeneity. `Chimeric' sequences possessing halves of markedly different AT composition elongate under fixed external conditions via distinct, spatially segregated transitions. The corresponding force-extension data display two plateaux at forces whose difference varies with pulling rate in a manner that depends qualitatively upon whether the hybridized S-form is accessible. This observation implies a test for S-DNA that could be performed in experiment. Our results suggest that qualitatively different, spatially segregated conformational transitions can occur at a single thermodynamic state within single molecules of DNA.

cond-mat.stat-mech↗
arXiv2008

Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles

We introduce a `virtual-move' Monte Carlo (VMMC) algorithm for systems of pairwise-interacting particles. This algorithm facilitates the simulation of particles possessing attractions of short range and arbitrary strength and geometry, an important realization being self-assembling particles endowed with strong, short-ranged and angularly specific (`patchy') attractions. Standard Monte Carlo techniques employ sequential updates of particles and suffer from low acceptance rates when attractions are strong. Our algorithm avoids this slowing-down by proposing simultaneous moves of collections (clusters) of particles according to gradients of interaction energies. One particle first executes a `virtual' trial move. We determine which of its neighbours move in a similar fashion by calculating individual bond energies before and after the proposed move. We iterate this procedure and update simultaneously the positions of all affected particles. Particles move according to an approximation of realistic dynamics without requiring the explicit computation of forces, and without the step size restrictions required when integrating equations of motion. We also employ a size- and shape-dependent hydrodynamic damping of cluster movements. We discuss the virtual-move algorithm in the context of other Monte Carlo cluster-move schemes, and demonstrate its utility by applying it to a model of biological self-assembly.

cond-mat.stat-mech↗
arXiv2008

The limits of filopodium stability

Filopodia are long, finger-like membrane tubes supported by cytoskeletal filaments. Their shape is determined by the stiffness of the actin filament bundles found inside them and by the interplay between the surface tension and bending rigidity of the membrane. Although one might expect the Euler buckling instability to limit the length of filopodia, we show through simple energetic considerations that this is in general not the case. By further analyzing the statics of filaments inside membrane tubes, and through computer simulations that capture membrane and filament fluctuations, we show under which conditions filopodia of arbitrary lengths are stable. We discuss several in vitro experiments where this kind of stability has already been observed. Furthermore, we predict that the filaments in long, stable filopodia adopt a helical shape.

q-bio.SC↗
arXiv2007

There and (slowly) back again: Entropy-driven hysteresis in a model of DNA overstretching

When pulled along its axis, double-stranded DNA elongates abruptly at a force of about 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to a molten state consisting of unhybridized single strands. The second picture instead introduces an elongated hybridized phase, called S-DNA, structurally and thermodynamically distinct from standard B-DNA. Little thermodynamic evidence exists to discriminate directly between these competing pictures. Here we show that within a microscopic model of DNA we can distinguish between the dynamics associated with each. In experiment, considerable hysteresis in a cycle of stretching and shortening develops as temperature is increased. Since there are few possible causes of hysteresis in a system whose extent is appreciable in only one dimension, such behavior offers a discriminating test of the two pictures of overstretching. Most experiments are performed upon nicked DNA, permitting the detachment (`unpeeling') of strands. We show that the long-wavelength progression of the unpeeled front generates hysteresis, the character of which agrees with experiment only if we assume the existence of S-DNA. We also show that internal melting (distinct from unpeeling) can generate hysteresis, the degree of which is strongly dependent upon the nonextensive loop entropy of single-stranded DNA.

cond-mat.stat-mech↗
arXiv2005

Two-stage coarsening mechanism in a kinetically constrained model of an attractive colloid

We study an attractive version of the East model using the real-space renormalization group (RG) introduced by Stella et al. The former is a kinetically constrained model with an Ising-like interaction between excitations, and shows striking agreement with the phenomonology of attractive colloidal systems. We find that the RG predicts two nonuniversal dynamic exponents, which suggests that in the out-of-equilibrium regime the model coarsens via a two-stage mechanism. We explain this mechanism physically, and verify this prediction numerically. In addition, we find that the characteristic relaxation time of the model is a non-monotonic function of attraction strength, again in agreement with numerical results.

cond-mat.stat-mech↗
arXiv2005

Equilibrium free energies from fast-switching trajectories with large time steps

Jarzynski's identity for the free energy difference between two equilibrium states can be viewed as a special case of a more general procedure based on phase space mappings. Solving a system's equation of motion by approximate means generates a mapping that is perfectly valid for this purpose, regardless of how closely the solution mimics true time evolution. We exploit this fact, using crudely dynamical trajectories to compute free energy differences that are in principle exact. Numerical simulations show that Newton's equation can be discretized to low order over very large time steps (limited only by the computer's ability to represent resulting values of dynamical variables) without sacrificing thermodynamic accuracy. For computing the reversible work required to move a particle through a dense liquid, these calculations are more efficient than conventional fast switching simulations by more than an order of magnitude. We also explore consequences of the phase space mapping perspective for systems at equilibrium, deriving an exact expression for the statistics of energy fluctuations in simulated conservative systems.

cond-mat.stat-mech↗
arXiv2005

Comparison of Dynamical Heterogeneity in Hard-Sphere and Attractive Glass Formers

Using molecular dynamics simulations, we have determined that the nature of dynamical heterogeneity in jammed liquids is very sensitive to short-ranged attractions. Weakly attractive systems differ little from dense hard-sphere and Lennard-Jones fluids: Particle motion is punctuated and tends to proceed in steps of roughly a single particle diameter. Both of these basic features change in the presence of appreciable attractions. Transient periods of particle mobility and immobility cannot be discerned at intermediate attraction strength, for which structural relaxation is greatly enhanced. Strong attractions, known to dramatically inhibit relaxation, restore bimodality of particle motion. But in this regime, transiently mobile particles move in steps that are significantly more biased toward large displacements than in the case of weak attractions. This modified feature of dynamic heterogeneity, which cannot be captured by conventional mode coupling theory, verifies recent predictions from a model of spatially correlated facilitating defects.

cond-mat.soft↗
arXiv2005

Short-ranged attractions in jammed liquids: How cooling can melt a glass

We demonstrate that an extended picture of kinetic constraints in glass-forming liquids is sufficient to explain dynamic anomalies observed in dense suspensions of strongly attracting colloidal particles. We augment a simple model of heterogeneous relaxation with static attractions between facilitating excitations, in a way that mimics the structural effect of short-ranged interparticle attractions. The resulting spatial correlations among facilitated and unfacilitated regions give rise to new relaxation mechanisms that account for non-monotonic dependence of relaxation times on attraction strength as well as logarithmic decay of density correlations in time. These unusual features are a simple consequence of spatial segregation of kinetic constraints, suggesting an alternative physical perspective on attractive colloids than that suggested by mode-coupling theory. Based on the behavior of our model, we predict a crossover from super-Arrhenius to Arrhenius temperature dependence as attractions become dominant at fixed packing fraction.

cond-mat.stat-mech↗
arXiv2003

The nature of slow dynamics in a minimal model of frustration-limited domains

We present simulation results for the dynamics of a schematic model based on the frustration-limited domain picture of glass-forming liquids. These results are compared with approximate theoretical predictions analogous to those commonly used for supercooled liquid dynamics. Although model relaxation times increase by several orders of magnitude in a non-Arrhenius manner as a microphase separation transition is approached, the slow relaxation is in many ways dissimilar to that of a liquid. In particular, structural relaxation is nearly exponential in time at each wave vector, indicating that the mode coupling effects dominating liquid relaxation are comparatively weak within this model. Relaxation properties of the model are instead well reproduced by the simplest dynamical extension of a static Hartree approximation. This approach is qualitatively accurate even for temperatures at which the mode coupling approximation predicts loss of ergodicity. These results suggest that the thermodynamically disordered phase of such a minimal model poorly caricatures the slow dynamics of a liquid near its glass transition.

cond-mat.stat-mech↗
arXiv2001

Mechanical response of random heteropolymers

We present an analytical theory for heteropolymer deformation, as exemplified experimentally by stretching of single protein molecules. Using a mean-field replica theory, we determine phase diagrams for stress-induced unfolding of typical random sequences. This transition is sharp in the limit of infinitely long chain molecules. But for chain lengths relevant to biological macromolecules, partially unfolded conformations prevail over an intermediate range of stress. These necklace-like structures, comprised of alternating compact and extended subunits, are stabilized by quenched variations in the composition of finite chain segments. The most stable arrangements of these subunits are largely determined by preferential extension of segments rich in solvophilic monomers. This predicted significance of necklace structures explains recent observations in protein stretching experiments. We examine the statistical features of select sequences that give rise to mechanical strength and may thus have guided the evolution of proteins that carry out mechanical functions in living cells.

cond-mat.stat-mech↗
arXiv2001

Reversible stretching of homopolymers and random heteropolymers

We have analyzed the equilibrium response of chain molecules to stretching. For a homogeneous sequence of monomers, the induced transition from compact globule to extended coil below the $θ$-temperature is predicted to be sharp. For random sequences, however, the transition may be smoothed by a prevalence of necklace-like structures, in which globular regions and coil regions coexist in a single chain. As we show in the context of a random copolymer, preferential solvation of one monomer type lends stability to such structures. The range of stretching forces over which necklaces are stable is sensitive to chain length as well as sequence statistics.

cond-mat.soft↗