We describe a highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue (Anderson and Glotzer, arXiv:1308.5587). Our approach is inspired by a traditional CPU-based code, LAMMPS (Plimpton, J. Comp. Phys. 117, 1995), but is implemented within a code that was designed for execution on GPUs from the start (Anderson et al., J. Comp. Phys. 227, 2008). The software supports short-ranged pair force and bond force fields and achieves optimal GPU performance using an autotuning algorithm. We are able to demonstrate equivalent or superior scaling on up to 3,375 GPUs in Lennard-Jones and dissipative particle dynamics (DPD) simulations of up to 108 million particles. GPUDirect RDMA capabilities in recent GPU generations provide better performance in full double precision calculations. For a representative polymer physics application, HOOMD-blue 1.0 provides an effective GPU vs. CPU node speed-up of 12.5×.
Simulations of five different coarse-grained models of symmetric diblock copolymer melts are compared to demonstrate a universal (i. e., model-independent) dependence of the free energy on the invariant degree of polymerization N , and to study universal properties of the order-disorder transition (ODT). The ODT appears to exhibit two regimes: Systems of very long chains (N > ∼ 10 4 ) are well described by the Fredrickson-Helfand theory, which assumes weak segregation near the ODT. Systems of smaller but experimentally relevant values, N < ∼ 10 4 , undergo a transition between strongly segregated disordered and lamellar phases that, though universal, is not adequately described by any existing theory.PACS numbers: 82.35. Jk,64.70.km,64.60.De Universality is a powerful feature of polymer statistical mechanics that allows the behavior of real systems to be predicted on the basis of simple generic models and scaling arguments. The paradigmatic example is the scaling theory of dilute and semidilute polymer solutions in good solvents [1][2][3], which predicts a universal dependence of all properties on two thermodynamic state parameters (an excluded volume parameter and an overlap parameter). Historically, this scaling hypothesis was verified by comparing experiments on diverse chemical systems with varied chain lengths and concentrations [3][4][5]. Here, we compare simulations of diverse models to verify an analogous scaling hypothesis about the equation of state and order-disorder transition (ODT) of symmetric diblock copolymers, and to characterize this transition.We consider a dense liquid of AB diblock copolymers, with N monomers per chain, and a fraction f A of A monomers. We focus on the symmetric case, f A = 1/2. Self-consistent field theory (SCFT) is the dominant theoretical approach for block copolymers [6][7][8]. SCFT describes polymers as random walks with a monomer statistical segment length b, which we take to be equal for A and B monomers. The free energy cost of contact between A and B monomers is characterized by an effective Flory-Huggins interaction parameter χ e . Let g denote a dimensionless excess free energy per chain, normalized by the thermal energy k B T . SCFT predicts a free energy g for each phase that depends only upon f A and the product χ e N , or upon χ e N alone for f A = 1/2. This yields a predicted phase diagram [6, 7] that likewise depends only on f A and χ e N . For f A = 1/2, SCFT predicts a transition between the disordered phase and lamellar phase at (χ e N ) ODT = 10.495.SCFT is believed to be exact in the limit of infinitely long, strongly interpenetrating polymers [9, 10]. The degree of interpenetration in a polymer liquid is characterized by a dimensionless concentration C ≡ cR 3 /N , in which c is monomer concentration, c/N is molecule concentration, and R = √ N b is coil size. Alternatively, interpenetration may be characterized by the invariant degree of polymerization. A series of post-SCF theories [10][11][12][13][14][15][16][17][18], starting with the Fredrickson...
We present a simulation study of how properties of symmetric diblock copolymers depend on the invariant degree of polymerization N̅, focusing on the vicinity of the order–disorder transition (ODT). Results from several coarse-grained simulation models are combined to cover a range of N̅ ≃ 200–8000 that includes most of the experimentally relevant range. Results are presented for the free energy per chain, the value of χe N at the ODT, the latent heat of transition, the layer spacing, the composition profile, and compression modulus in the ordered phase. Universality (i.e., model independence) is demonstrated by showing that equivalent results for all properties are obtained from corresponding thermodynamic states of different simulation models. Corresponding states of symmetric copolymers are states with equal values of the parameters χe N and N̅, where χe is an effective Flory–Huggins interaction parameter and N is a degree of polymerization. The underlying universality becomes apparent, however, only if data are analyzed using an adequate estimate of χe, which we obtain by fitting the structure factor in the disordered state to recent theoretical predictions. The results show that behavior near the ODT exhibits a different character at moderate and high values of N̅, with a crossover near N̅ ≃ 104. Within the range N̅ ≲ 104 studied here, the ordered and disordered phases near the ODT both contain strongly segregated domains of nearly pure A and B, in contrast to the assumption of weak segregation underlying the Fredrickson–Helfand (FH) theory. In this regime, the FH theory is inaccurate and substantially underestimates the value of χe N at the ODT. Results for the highest values of N̅ studied here agree reasonably well with FH predictions, suggesting that the theory may be accurate for N̅ ≳ 104. Self-consistent field theory (SCFT) grossly underestimates (χe N)ODT for modest N̅ because it cannot describe strong correlations in the disordered phase. SCFT is found, however, to yield accurate predictions for several properties of the ordered lamellar phase.
The unique mechanical performance of animal cells and tissues is attributed mostly to their internal biopolymer meshworks. Its perplexing universality and robustness against structural modifications by drugs and mutations is an enigma in cell biology and provides formidable challenges to materials science. Recent investigations could pinpoint highly universal patterns in the soft glassy rheology and nonlinear elasticity of cells and reconstituted networks. Here, we report observations of a glass transition in semidilute F-actin solutions, which could hold the key to a unified explanation of these phenomena. Combining suitable rheological protocols with high-precision dynamic light scattering, we can establish a remarkable rheological redundancy and trace it back to a highly universal exponential stretching of the single-polymer relaxation spectrum of a ''glassy wormlike chain.'' By exploiting the ensuing generalized time-temperature superposition principle, the time domain accessible to microrheometry can be extended by several orders of magnitude, thus opening promising new metrological opportunities.biopolymers ͉ light scattering ͉ nonlinear rheology ͉ wormlike chain A major strategy in the investigation of complex materials is to reassemble them step by step from simpler subunits to trace back their material properties on the macroscopic scale to those of their elementary constituents. This strategy has been successfully applied to the biopolymer networks that constitute the basic scaffolding structure of animal cells, known as the cytoskeleton (1). Filamentous actin (F-actin), the major loadbearing element of the cytoskeleton has received particular attention. The success of simple viscoelastic models in the quantitative analysis of the rheological behavior of in vitro reconstituted biopolymer networks (1-5) has rendered them an attractive paradigm for rationalizing the mechanics of live cells (6, 7). Indeed, there appear to be striking mechanical analogies between cells and prestressed reconstituted networks (7-9) and strong correlations of cell functions with the viscoelastic parameters, suggesting the latter as viable indices for clinical diagnosis (10). Recently, this widely shared view has been challenged by observations (11) that live cells obey the highly universal and comparatively featureless pattern of ''soft glassy rheology'' that is ubiquitous in soft condensed matter (12). These observations seem to imply that the pertinent linear mechanical properties of a cell might be composed in a single number, the so-called ''noise temperature'' (13) of the glass, and on this basis it has indeed been suggested that we are all built of glass (14). Subsequently, it has become a central task in cell biophysics to understand how the two conflicting paradigms might be integrated into a unified picture (15-17).Here, we aim to resolve the apparent puzzle by demonstrating that highly purified in vitro polymerized semidilute F-actin solutions undergo a glass transition as a function of various physiologically relev...
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