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Water Networks in Photosystem II Using Crystalline Molecular Dynamics Simulations and Room-Temperature XFEL Serial Crystallography
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Physical properties of the HIV-1 capsid from all-atom molecular dynamics simulations
Human immunodeficiency virus type 1 (HIV-1) infection is highly dependent on its capsid. The capsid is a large container, made of B 1,300 proteins with altogether 4 million atoms. Though the capsid proteins are all identical, they nevertheless arrange themselves into a largely asymmetric structure made of hexamers and pentamers. The large number of degrees of freedom and lack of symmetry pose a challenge to studying the chemical details of the HIV capsid. Simulations of over 64 million atoms for over 1 μs allow us to conduct a comprehensive study of the chemical–physical properties of an empty HIV-1 capsid, including its electrostatics, vibrational and acoustic properties, and the effects of solvent (ions and water) on the capsid. Furthermore, the simulations reveal critical details about the capsid with implications to biological function.
Implementing reactivity in molecular dynamics simulations with harmonic force fields
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Molecular recognition and specificity of biomolecules to titanium dioxide from molecular dynamics simulations
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A primer on selecting grain boundary sets for comparison of interfacial fracture properties in molecular dynamics simulations
In this study, all grain boundaries are not equal in their predisposition for fracture due to the complex coupling between lattice geometry, interfacial structure, and mechanical properties. The ability to understand these relationships is crucial to engineer materials resilient to grain boundary fracture. Here, a methodology is presented to isolate the role of grain boundary structure on interfacial fracture properties, such as the tensile strength and work of separation, using atomistic simulations. Instead of constructing sets of grain boundary models within the misorientation/structure space by simply varying the misorientation angle around a fixed misorientation axis, the proposed method creates sets of grain boundary models by means of isocurves associated with important fracture-related properties of the adjoining lattices. Such properties may include anisotropic elastic moduli, the Schmid factor for primary slip, and the propensity for simultaneous slip on multiple slip systems. This approach eliminates the effect of lattice properties from the comparative analysis of interfacial fracture properties and thus enables the identification of structure-property relationships for grain boundaries. As an example, this methodology is implemented to study crack propagation along Ni grain boundaries. Segregated H is used as a means to emphasize differences in the selected grain boundary structures while keeping lattice properties fixed.
Molecular dynamics simulations of propane in slit shaped silica nano-pores: direct comparison with quasielastic neutron scattering experiments
MD simulations reveal the origin of anomalous pressure dependence of propane diffusion in silica mesopores.
Analysis of an all-solid state nanobattery using molecular dynamics simulations under an external electric field
Present Li-ion battery (LIB) technology requires strong improvements in performance, energy capacity, charging-time, and cost to expand their application to e-mobility and grid storage. Li-metal is one of the most promising materials to replace commercial anodes such as graphite because of its 10 times higher specific capacity. However, Li-metal has high reactivity with commercial liquid electrolytes; thus, new solid materials are proposed to replace liquid electrolytes when Li-metal anodes are used. We present a theoretical analysis of the charging process in a full nanobattery, containing a LiCoO 2 cathode, a Li 7 P2S 8 I solid-state electrolyte (SSE), a Li-metal anode as well as Al and Cu collectors for the cathode and anode, respectively. In addition, we added a Li 3 P/Li 2 S film as a solid electrolyte interphase (SEI) layer between the Li-anode and SSE. Thus, we focus this study on the SEI and SSE. We simulated the charging of the nanobattery with an external voltage by applying an electric field. We estimated temperature profiles within the nanobattery and analyzed Li-ion transport through the SSE and SEI. Here, we observed a slight temperature rise at the SEI due to reactions forming $PS_{3}^{–}$ and $P_{2}S_{7}^{4}$$^{–}$ fragments at the interfaces; however, this temperature profile changes due to the charging current under the presence of the external electric field ε = 0.75 V Å –1 . Without the external field, the calculated open-circuit voltage (OCV) was 3.86 V for the battery, which is within the range of values of commercial cobalt-based LIBs. This voltage implies a spontaneous fall of available Li-ions from the anode to the cathode (during discharge). The charge of this nanobattery requires overcoming the OCV plus an additional voltage that determines the charging current. Thus, we applied an external potential able to neutralize the OCV, plus an additional 1.6 V to induce the transport of Li + from the cathode up to the anode. Several interesting details about Li + transport paths through the SSE and SEI are discussed.
Coarse-grained force-field for large scale molecular dynamics simulations of polyacrylamide and polyacrylamide-gels based on quantum mechanics
Developing a coarse-grained force field for polyacrylamide based on quantum mechanics equation of state.
Data-driven molecular dynamics simulation of water isotope separation using a catalytically active ultrathin membrane
Water isotope separation, specifically separating heavy from light water, is a technologically important problem due to the usage of heavy water in applications such as nuclear magnetic resonance, nuclear power, and spectroscopy.
Coarse-grained molecular dynamics simulations of mixtures of polysulfamides
We present a new coarse-grained model and molecular simulation study of polysulfamide, a new class of polymer that could be a sustainable alternative to commodity polymers like polyurea.
Transient-absorption spectroscopy of dendrimers via nonadiabatic excited-state dynamics simulations
The efficiency of light-harvesting and energy transfer in multi-chromophore ensembles underpins natural photosynthesis.
Understanding ionic transport in perovskite lithium-ion conductor Li 3/8 Sr 7/16 Ta 3/4 Hf 1/4 O 3 : a neutron diffraction and molecular dynamics simulation study
Solid-state Li-ion electrolytes (SSEs) are essential for the development of next-generation solid-state Li-metal batteries and new Li-extraction electrochemical cells.
Well-balanced treatment of gravity in astrophysical fluid dynamics simulations at low Mach numbers
We report accurate simulations of flows in stellar interiors are crucial to improving our understanding of stellar structure and evolution. Because the typically slow flows are merely tiny perturbations on top of a close balance between gravity and the pressure gradient, such simulations place heavy demands on numerical hydrodynamics schemes. We demonstrate how discretization errors on grids of reasonable size can lead to spurious flows orders of magnitude faster than the physical flow. Well-balanced numerical schemes can deal with this problem. Three such schemes were applied in the implicit, finite-volume SEVEN-LEAGUE HYDRO code in combination with a low-Mach-number numerical flux function. We compare how the schemes perform in four numerical experiments addressing some of the challenges imposed by typical problems in stellar hydrodynamics. We find that the α-β and deviation well-balancing methods can accurately maintain hydrostatic solutions provided that gravitational potential energy is included in the total energy balance. They accurately conserve minuscule entropy fluctuations advected in an isentropic stratification, which enables the methods to reproduce the expected scaling of convective flow speed with the heating rate. The deviation method also substantially increases accuracy of maintaining stationary orbital motions in a Keplerian disk on long timescales. The Cargo–LeRoux method fares substantially worse in our tests, although its simplicity may still offer some merits in certain situations. Overall, we find the well-balanced treatment of gravity in combination with low Mach number flux functions essential to reproducing correct physical solutions to challenging stellar slow-flow problems on affordable collocated grids.