gmxapi: A GROMACS-native Python interface for molecular dynamics with ensemble and plugin support.

Gmxapi provides an integrated, native Python API for both standard and advanced molecular dynamics simulations in GROMACS. The Python interface permits multiple levels of integration with the core GROMACS libraries, and legacy support is provided via an interface that mimics the command-line syntax, so that all GROMACS commands are fully available. Gmxapi has been officially supported since the GROMACS 2019 release and is enabled by default in current versions of the software. Here we describe gmxapi 0.3 and later. Beyond simply wrapping GROMACS library operations, the API permits several advanced operations that are not feasible using the prior command-line interface. First, the API allows custom user plugin code within the molecular dynamics force calculations, so users can execute custom algorithms without modifying the GROMACS source. Second, the Python interface allows tasks to be dynamically defined, so high-level algorithms for molecular dynamics simulation and analysis can be coordinated with loop and conditional operations. Gmxapi makes GROMACS more accessible to custom Python scripting while also providing support for high-level data-flow simulation algorithms that were previously feasible only in external packages.

gmxapi: a high-level interface for advanced control and extension of molecular dynamics simulations.

Summary: Molecular dynamics simulations have found use in a wide variety of biomolecular applications, from protein folding kinetics to computational drug design to refinement of molecular structures. Two areas where users and developers frequently need to extend the built-in capabilities of most software packages are implementing custom interactions, for instance biases derived from experimental data, and running ensembles of simulations. We present a Python high-level interface for the popular simulation package GROMACS that i) allows custom potential functions without modifying the simulation package code, ii) maintains the optimized performance of GROMACS and iii) presents an abstract interface to building and executing computational graphs that allows transparent low-level optimization of data flow and task placement. Minimal dependencies make this integrated API for the GROMACS simulation engine simple, portable and maintainable. We demonstrate this API for experimentally-driven refinement of protein conformational ensembles. Availability and implementation: LGPLv2.1 source and instructions are available at https://github.com/kassonlab/gmxapi. Supplementary information: Supplementary data are available at Bioinformatics online.

Visfatin alters the cytokine and matrix-degrading enzyme profile during osteogenic and adipogenic MSC differentiation.

OBJECTIVES: Age-related bone loss is associated with bone marrow adiposity. Adipokines (e.g., visfatin, resistin, leptin) are adipocyte-derived factors with immunomodulatory properties and might influence differentiation of bone marrow-derived mesenchymal stem cells (MSC) in osteoarthritis (OA) and osteoporosis (OP). Thus, the presence of adipokines and MMPs in bone marrow and their effects on MSC differentiation were analyzed. METHODS: MSC and ribonucleic acid (RNA) were isolated from femoral heads after hip replacement surgery of OA or osteoporotic femoral neck fracture (FF) patients. Bone structural parameters were evaluated by microcomputed tomography (µCT). MSC were differentiated towards adipocytes or osteoblasts with/without adipokines. Gene expression (adipokines, bone marker genes, MMPs, TIMPs) and cytokine production was evaluated by realtime-polymerase chain reaction (realtime-PCR) and enzyme-linked immunosorbent assay (ELISA). Matrix mineralization was quantified using Alizarin red S staining. RESULTS: µCT showed an osteoporotic phenotype of FF compared to OA bone (reduced trabecular thickness and increased ratio of bone surface vs volume of solid bone). Visfatin and leptin were increased in FF vs OA. Visfatin induced the secretion of IL-6, IL-8, and MCP-1 during osteogenic and adipogenic differentiation. In contrast to resistin and leptin, visfatin increased MMP2 and MMP13 during adipogenesis. In osteogenically differentiated cells, MMPs and TIMPs were reduced by visfatin. Visfatin significantly increased matrix mineralization during osteogenesis, whereas collagen type I expression was reduced. CONCLUSION: Visfatin-mediated increase of matrix mineralization and reduced collagen type I expression could contribute to bone fragility. Visfatin is involved in impaired bone remodeling at the adipose tissue/bone interface through induction of proinflammatory factors and dysregulated MMP/TIMP balance during MSC differentiation.

Virial Coefficients and Equations of State for Hard Polyhedron Fluids.

Hard polyhedra are a natural extension of the hard sphere model for simple fluids, but there is no general scheme for predicting the effect of shape on thermodynamic properties, even in moderate-density fluids. Only the second virial coefficient is known analytically for general convex shapes, so higher-order equations of state have been elusive. Here we investigate high-precision state functions in the fluid phase of 14 representative polyhedra with different assembly behaviors. We discuss historic efforts in analytically approximating virial coefficients up to B4 and numerically evaluating them to B8. Using virial coefficients as inputs, we show the convergence properties for four equations of state for hard convex bodies. In particular, the exponential approximant of Barlow et al. (J. Chem. Phys. 2012, 137, 204102) is found to be useful up to the first ordering transition for most polyhedra. The convergence behavior we explore can guide choices in expending additional resources for improved estimates. Fluids of arbitrary hard convex bodies are too complicated to be described in a general way at high densities, so the high-precision state data we provide can serve as a reference for future work in calculating state data or as a basis for thermodynamic integration.

Quasicrystalline nanocrystal superlattice with partial matching rules.

Expanding the library of self-assembled superstructures provides insight into the behaviour of atomic crystals and supports the development of materials with mesoscale order. Here we build on recent findings of soft matter quasicrystals and report a quasicrystalline binary nanocrystal superlattice that exhibits correlations in the form of partial matching rules reducing tiling disorder. We determine a three-dimensional structure model through electron tomography and direct imaging of surface topography. The 12-fold rotational symmetry of the quasicrystal is broken in sublayers, forming a random tiling of rectangles, large triangles and small triangles with 6-fold symmetry. We analyse the geometry of the experimental tiling and discuss factors relevant for the stabilization of the quasicrystal. Our joint experimental-computational study demonstrates the power of nanocrystal superlattice engineering and further narrows the gap between the richness of crystal structures found with atoms and in soft matter assemblies.