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Register a new userAccurate implementation of leaping in space: The spatial partitioned-leaping algorithm
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There is a great need for accurate and efficient computational approaches that can account for both the discrete and stochastic nature of chemical interactions as well as spatial inhomogeneities and diffusion. This is particularly true in biology and nanoscale materials science, where the common assumptions of deterministic dynamics and well-mixed reaction volumes often break down. In this article, we present a spatial version of the partitioned-leaping algorithm (PLA), a multiscale accelerated-stochastic simulation approach built upon the tau-leaping framework of Gillespie. We pay special attention to the details of the implementation, particularly as it pertains to the time step calculation procedure. We point out conceptual errors that have been made in this regard in prior implementations of spatial tau-leaping and illustrate the manifestation of these errors through practical examples. Finally, we discuss the fundamental difficulties associated with incorporating efficient exact-stochastic techniques, such as the next-subvolume method, into a spatial-leaping framework and suggest possible solutions.
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Leaping methods show great promise for significantly accelerating stochastic simulations of complex biochemical reaction networks. However, few practical applications of leaping have appeared in the literature to date. Here, we address this issue using the partitioned leaping algorithm (PLA) [L.A. Harris and P. Clancy, J. Chem. Phys. 125, 144107 (2006)], a recently-introduced multiscale leaping approach. We use the PLA to investigate stochastic effects in two model biochemical reaction networks. The networks that we consider are simple enough so as to be accessible to our intuition but sufficiently complex so as to be generally representative of real biological systems. We demonstrate how the PLA allows us to quantify subtle effects of stochasticity in these systems that would be difficult to ascertain otherwise as well as not-so-subtle behaviors that would strain commonly-used exact stochastic methods. We also illustrate bottlenecks that can hinder the approach and exemplify and discuss possible strategies for overcoming them. Overall, our aim is to aid and motivate future applications of leaping by providing stark illustrations of the benefits of the method while at the same time elucidating obstacles that are often encountered in practice.
Multifocal microscopy (MFM) offers high-speed three-dimensional imaging through the simultaneous image capture from multiple focal planes. Conventional MFM systems use a fabricated grating in the emission path for a single emission wavelength band and one set of focal plane separations. While a Spatial Light Modulator (SLM) can add more flexibility, the relatively small number of pixels in the SLM chip, cross-talk between the pixels, and aberrations in the imaging system can produce non-uniform intensity in the different axially separated image planes. We present an in situ iterative SLM calibration algorithm that overcomes these optical- and hardware-related limitations to deliver near-uniform intensity across all focal planes. Using immobilized gold nanoparticles under darkfield illumination, we demonstrate superior intensity evenness compared to current methods. We also demonstrate applicability across emission wavelengths, axial plane separations, imaging modalities, SLM settings, and different SLM manufacturers. Therefore, our microscope design and algorithms provide an alternative to fabricated gratings in MFM, as they are relatively simple and could find broad applications in the wider research community.
Most widely used density functional approximations suffer from self-interaction (SI) error, which can be corrected using the Perdew-Zunger (PZ) self-interaction correction (SIC). We implement the recently proposed size-extensive formulation of PZ-SIC using Fermi-Lowdin Orbitals (FLOs) in real space, which is amenable to systematic convergence and large-scale parallelization. We verify the new formulation within the generalized Slater scheme by computing atomization energies and ionization potentials of selected molecules and comparing to those obtained by existing FLOSIC implementations in Gaussian based codes. The results show good agreement between the two formulations, with new real-space results somewhat closer to experiment on average for the systems considered. We also obtain the ionization potentials and atomization energies by scaling down the Slater statistical average of SIC potentials. The results show that scaling down the average SIC potential improves both atomization energies and ionization potentials, bringing them closer to experiment. Finally, we verify the present formulation by calculating the barrier heights of chemical reactions in the BH6 dataset, where significant improvements are obtained relative to Gaussian based FLOSIC results.
Single-particle imaging with X-ray free-electron lasers depends crucially on algorithms that merge large numbers of weak diffraction patterns despite missing measurements of parameters such as particle orientations. The Expand-Maximize-Compress (EMC) algorithm is highly effective at merging single-particle diffraction patterns with missing orientation values, but most implementations exhaustively sample the space of missing parameters and may become computationally prohibitive as the number of degrees of freedom extend beyond orientation angles. Here we describe how the EMC algorithm can be modified to employ Metropolis Monte Carlo sampling rather than grid sampling, which may be favorable for cases with more than three missing parameters. Using simulated data, this variant is compared to the standard EMC algorithm. Higher dimensional cases of mixed target species and variable x-ray fluence are also explored.
The Alchemical Transfer Method (ATM) for the calculation of standard binding free energies of non-covalent molecular complexes is presented. The method is based on a coordinate displacement perturbation of the ligand between the receptor binding site and the explicit solvent bulk, and a thermodynamic cycle connected by a symmetric intermediate in which the ligand interacts with the receptor and solvent environments with equal strength. While the approach is alchemical, the implementation of ATM is as straightforward as for physical pathway methods of binding. The method is applicable in principle with any force field, it does not require splitting the alchemical transformations into electrostatic and non-electrostatic steps, and it does not require soft-core pair potentials. We have implemented ATM as a freely available and open-source plugin of the OpenMM molecular dynamics library. The method and its implementation are validated on the SAMPL6 SAMPLing host-guest benchmark set. The work paves the way to streamlined alchemical relative and absolute binding free energy implementations on many molecular simulation packages and with arbitrary energy functions including polarizable, quantum-mechanical, and artificial neural network potentials.
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