A systematic method to calculate anharmonic force constants of crystals is presented. The method employs the direct-method approach, where anharmonic force constants are extracted from the trajectory ...of first-principles molecular dynamics simulations at high temperature. The method is applied to Si where accurate cubic and quartic force constants are obtained. We observe that higher-order correction is crucial to obtain accurate force constants from the trajectory with large atomic displacements. The calculated harmonic and anharmonic force constants are, then, combined with the Boltzmann transport equation (BTE) and non-equilibrium molecular dynamics (NEMD) methods in calculating the thermal conductivity. The BTE approach successfully predicts the lattice thermal conductivity of bulk Si, whereas NEMD shows considerable underestimates. To evaluate the linear extrapolation method employed in NEMD to estimate bulk values, we analyze the size dependence in NEMD based on BTE calculations. We observe strong nonlinearity in the size dependence of NEMD in Si, which can be ascribed to acoustic phonons having long mean-free-paths and carrying considerable heat. Subsequently, we also apply the whole method to a thermoelectric material Mg2Si and demonstrate the reliability of the NEMD method for systems with low thermal conductivities.
The radiation intensity of the outer shell of a carbon onion complex containing an ionized iron atom is calculated according to the scheme proposed by L. D. Landau. A complete description of the ...oscillations arising in the system under consideration is given. Keywords: molecular dynamics, dipole radiation, mathematical modeling.
This work presents Neural Equivariant Interatomic Potentials (NequIP), an E(3)-equivariant neural network approach for learning interatomic potentials from ab-initio calculations for molecular ...dynamics simulations. While most contemporary symmetry-aware models use invariant convolutions and only act on scalars, NequIP employs E(3)-equivariant convolutions for interactions of geometric tensors, resulting in a more information-rich and faithful representation of atomic environments. The method achieves state-of-the-art accuracy on a challenging and diverse set of molecules and materials while exhibiting remarkable data efficiency. NequIP outperforms existing models with up to three orders of magnitude fewer training data, challenging the widely held belief that deep neural networks require massive training sets. The high data efficiency of the method allows for the construction of accurate potentials using high-order quantum chemical level of theory as reference and enables high-fidelity molecular dynamics simulations over long time scales.
The electrochemical N2 reduction reaction (NRR) offers a promising approach for sustainable NH3 production, and modulating the structural/electronic configurations of the catalyst materials with ...optimized electrocatalytic properties is pivotal for achieving high‐efficiency NRR electrocatalysis. Herein, vacancy and heterostructure engineering are rationally integrated to explore O‐vacancy‐rich MoO3‐x anchored on Ti3C2Tx‐MXene (MoO3‐x/MXene) as a highly active and selective NRR electrocatalyst, achieving an exceptional NRR activity with an NH3 yield of 95.8 µg h−1 mg−1 (−0.4 V) and a Faradaic efficiency of 22.3% (−0.3 V). A combination of in situ spectroscopy, molecular dynamics simulations and density functional theory computations is employed to unveil the synergistic effect of O‐vacancies and heterostructures for the NRR, which demonstrates that O‐vacancies on MoO3‐x serve as the active sites for N2 chemisorption and activation, while the MXene substrate can further regulate the O‐vacancy sites to break the scaling relation to effectively stabilize *N2/*N2H while destabilizing *NH2/*NH3, resulting in more optimized binding affinity of NRR intermediates toward reduced energy barriers and an enhanced NRR activity for MoO3‐x/MXene.
Multiple in situ spectroscopic experiments, molecular dynamics simulations and density functional theory computations unveil the synergistic effects of O‐vacancies (OVs) and heterostructures for the nitrogen reduction reaction (NRR) using MoO3‐x/MXene. OVs are the active sites for N2 chemisorption and activation, while MXene further modulates the OV sites to break the scaling relation to effectively stabilize *N2/*N2H while destabilizing *NH2/*NH3, resulting in reduced energy barriers and a boosted NRR activity.
Cancer cells can evade immune surveillance through binding of its transmembrane receptor CD47 to CD172a on myeloid cells. CD47 is recognized as a promising immune checkpoint for cancer immunotherapy ...inhibiting macrophage phagocytosis. N-terminal post-translated modification (PTM) via glutaminyl cyclase is a landmark event in CD47 function maturation, but the molecular mechanism underlying the mechano-chemical regulation of the modification on CD47/CD172a remains unclear. Here, we performed so-called "ramp-clamp" steered molecular dynamics (SMD) simulations, and found that the N-terminal PTM enhanced interaction of CD172a with CD47 by inducing a dynamics-driven contraction of the binding pocket of the bound CD172a, an additional constraint on CYS15 on CD47 significantly improved the tensile strength of the complex with or without PTM, and a catch bond phenomenon would occur in complex dissociation under tensile force of 25 pN in a PTM-independent manner too. The residues GLN52 and SER66 on CD172a reinforced the H-bonding with their partners on CD47 in responding to PTM, while ARG69 on CD172 with its partner on CD47 might be crucial in the structural stability of the complex. This work might serve as molecular basis for the PTM-induced function improvement of CD47, should be helpful for deeply understanding CD47-relevant immune response and cancer development, and provides a novel insight in developing of new strategies of immunotherapy targeting this molecule interaction.
Dyneins are an AAA+ motor responsible for motility and force generation toward the minus end of microtubules. Dynein motility is powered by nucleotide-dependent transitions of its linker domain, ...which transitions between straight (post-powerstroke) and bent (pre-powerstroke) conformations. To understand the dynamics and energetics of the linker, we performed all-atom molecular dynamics simulations of human dynein-2 primed for its power stroke. Simulations revealed that the linker can adopt either a bent conformation or a semi-bent conformation, separated by a 5.7 kT energy barrier. The linker cannot switch back to its straight conformation in the pre-powerstroke state due to a steric clash with the AAA+ ring. Simulations also showed that an isolated linker has a free energy minimum near the semi-bent conformation in the absence of the AAA+ ring, indicating that the linker stores energy as it bends and releases this energy during the powerstroke.
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•The priming stroke of dynein is modeled using all-atom MD simulations•The linker stores energy in its bent conformation•The linker can adopt a semi-bent conformation in the pre-powerstroke state•Straightening of the linker is gated due to a steric clash with the AAA+ ring
Dynein motility is powered by the swinging motion of its linker domain at the surface of the AAA+ ring. Modeling studies by Golcuk et al. found that the linker can attain two distinct bent conformations and cannot straighten due to the steric clash with the pre-powerstroke conformation of the ring.
The overexpression of p21-activated kinase 4 (PAK4) is associated with a variety of cancers. In this paper, the binding modes and inhibitory mechanisms of four 7H-pyrrolo2,3-dpyrimidine competitive ...inhibitors of PAK4 were investigated at the molecular level, mainly using molecular dynamics simulations and binding free energy calculations. The results show that the inhibitors had strong interactions with the hinge region, the β-sheets, and the residues with charged side chains around the 4-substituent. The terminal amino group of the inhibitor 5n was different from the other three, which could cause the enhancement of hydrogen bonds or electrostatic interactions formed with the surrounding residues. Thus, inhibitor 5n had the strongest inhibition capacity. The different halogen atoms on the 2-substituents of the inhibitors 5h, 5g, and 5e caused differences in the positions of the 2-benzene rings and affected the interactions of the hinge region. It also affected to some extent the orientations of the 4-imino groups and consequently their affinities for the surrounding charged residues. The combined results lead to the weakest inhibitory capacity of inhibitor 5e.
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