arXiv subjects

Jens Glaser

Publications and source records attributed to Jens Glaser.

8 recordsLinked to original sources

arXiv2019

HOOMD-blue: A Python package for high-performance molecular dynamics and hard particle Monte Carlo simulations

HOOMD-blue is a particle simulation engine designed for nano- and colloidal-scale molecular dynamics and hard particle Monte Carlo simulations. It has been actively developed since March 2007 and available open source since August 2008. HOOMD-blue is a Python package with a high performance C++/CUDA backend that we built from the ground up for GPU acceleration. The Python interface allows users to combine HOOMD-blue with with other packages in the Python ecosystem to create simulation and analysis workflows. We employ software engineering practices to develop, test, maintain, and expand the code.

physics.comp-ph↗

arXiv2019

Looped liquid-liquid coexistence in protein crystallization

In view of the notorious complexity of protein--protein interactions, simplified models of proteins treated as patchy particles offer a promising strategy to obtain insight into the mechanism of crystallization. Here we report liquid--liquid phase separation (LLPS) with a highly asymmetric coexistence region in a computational model of rubredoxin with real molecular shape. The coexistence region terminates in both an upper (UCST) and a lower (LCST) critical solution temperature, and the complex molecular shape explains the closed-loop behavior of the LLPS.

cond-mat.soft↗

arXiv2016

Using Depletion to Control Colloidal Crystal Assemblies of Hard Cuboctahedra

Depletion interactions arise from entropic forces, and their ability to induce aggregation and even ordering of colloidal particles through self-assembly is well established, especially for spherical colloids. We vary the size and concentration of penetrable hard sphere depletants in a system of cuboctahedra, and we show how depletion changes the preferential facet alignment of the colloids and thereby selects different crystal structures. Moreover, we explain the cuboctahedra phase behavior using perturbative free energy calculations. We find that cuboctahedra can form a stable simple cubic phase, and, remarkably, that the stability of this phase can only be rationalized by considering the effects of both the colloid and depletant entropy. We corroborate our results by analyzing how the depletant concentration and size affect the emergent directional entropic forces and hence the effective particle shape. We propose the use of depletants as a means of easily changing the effective shape of self-assembling anisotropic colloids.

cond-mat.soft↗

arXiv2015

A parallel algorithm for implicit depletant simulations

We present an algorithm to simulate the many-body depletion interaction between anisotropic colloids in an implicit way, integrating out the degrees of freedom of the depletants, which we treat as an ideal gas. Because the depletant particles are statistically independent and the depletion interaction is short-ranged, depletants are randomly inserted in parallel into the excluded volume surrounding a single translated and/or rotated colloid. A configurational bias scheme is used to enhance the acceptance rate. The method is validated and benchmarked both on multi-core CPUs and graphics processing units (GPUs) for the case of hard spheres, hemispheres and discoids. With depletants, we report novel cluster phases, in which hemispheres first assemble into spheres, which then form ordered hcp/fcc lattices. The method is significantly faster than any method without cluster moves and that tracks depletants explicitly, for systems of colloid packing fraction $ϕ_c<0.50$, and additionally enables simulation of the fluid-solid transition.

cond-mat.soft↗

arXiv2014

Strong scaling of general-purpose molecular dynamics simulations on GPUs

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 12.5x.

physics.comp-ph↗

arXiv2014

Universality of Block Copolymer Melts

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 $\overline{N}$, and to study universal properties of the order-disorder transition (ODT). The ODT appears to exhibit two regimes: Systems of very long chains ($\overline{N} \gtrsim 10^{4}$) are well described by the Fredrickson-Helfand theory, which assumes weak segregation near the ODT. Systems of smaller but experimentally relevant values, $\overline{N} \lesssim 10^4$, undergo a transition between strongly segregated disordered and lamellar phases that, though universal, is not adequately described by any existing theory.

cond-mat.soft↗

arXiv2012

Test of a scaling hypothesis for the structure factor of disordered diblock copolymer melts

Coarse-grained theories of dense polymer liquids such as block copolymer melts predict a universal dependence of equilibrium properties on a few dimensionless parameters. For symmetric diblock copolymer melts, such theories predict a universal dependence on only chi N and Nbar, where chi is an effective interaction parameter, N is a degree of polymerization, and Nbar is a measure of overlap. We test whether simulation results for the structure factor S(q) obtained from several different simulation models are consistent with this two-parameter scaling hypothesis. We compare results from three models: (1) a lattice Monte Carlo model, the bond-fluctuation model, (2) a bead-spring model with harsh repulsive interactions, similar to that of Kremer and Grest, and (3) a bead-spring model with very soft repulsion between beads, and strongly overlapping beads. We compare results from pairs of simulations of different models that have been designed to have matched values of Nbar, over a range of values of chi N and N, and devise methods to test the scaling hypothesis without relying on any prediction for how the phenomenological interaction parameter chi depends on more microscopic parameters. The results strongly support the scaling hypothesis, even for rather short chains, confirming that it is indeed possible to give an accurate universal description of simulation models that differ in many details.

cond-mat.soft↗

arXiv2011

Tube width fluctuations of entangled stiff polymers

The tube-like cages of stiff polymers in entangled solutions have been shown to exhibit characteristic spatial heterogeneities. We explain these observations by a systematic theory generalizing previous work by D. Morse (Phys. Rev. E 63:031502, 2001). With a local version of the binary collision approximation (BCA), the distribution of confinement strengths is calculated, and the magnitude and the distribution function of tube radius fluctuations are predicted. Our main result is a unique scaling function for the tube radius distribution, in good agreement with experimental and simulation data.

cond-mat.soft↗