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Shuttle-assisted charge transfer is pivotal for the efficient energy transduction from the food-stuff electrons to protons in the respiratory chain of animal cells and bacteria. The respiratory chain consists of four metalloprotein…
Hydrogenase occupy a central place in the energy metabolism of anaerobic bacteria. Although the structure of mitochondrial complex I is similar to that of hydrogenase, whether it has hydrogen metabolic activity remain unclear. Here, we show…
Active ion transport is very critical for living cells to maintain and regular internal and external environment. It is known that adenosine 5'-triphosphate (ATP) is a general energy source that applies bond energy for pumps to overcome ion…
Based on a quasi-one-dimensional limit of quantum Hall states on a thin torus, we construct a model of interaction-induced topological pumping which mimics the Hall response of the bosonic integer quantum Hall (BIQH) state. The…
Using a neural network potential (ANI-1ccx) generated from quantum data on a large data set of molecules and pairs of molecules, isothermal, constant volume simulations demonstrate that the model can be as accurate as ab initio molecular…
Many biological electron transfer (ET) reactions are mediated by metal centres in proteins. NADH:ubiquinone oxidoreductase (complex I) contains an intramolecular chain of seven iron-sulphur (FeS) clusters, one of the longest chains of metal…
Hydroxide ion transport in anion-exchange membranes fundamentally limits the efficiency of alkaline water electrolysis for green hydrogen production, yet the atomic-scale transport mechanisms remain poorly understood due to the…
Small organic molecules are thought to provide building blocks for the formation of complex interstellar polycyclic aromatic hydrocarbons (PAHs). However, the underlying chemical mechanisms remain unclear, particularly concerning the role…
Kohn-Sham density functional theory and plane wave basis set based ab initio molecular dynamics (AIMD) simulation is a powerful tool for studying complex reactions in solutions, such as electron transfer (ET) reactions involving…
Studies of nanoscale biological transport often use a mean-field approximation that is exact only when the system is at equilibrium and there are no interactions between particles on different sites in the network. We explore the…
Water diffusion through membrane proteins is a key aspect of cellular function. Essential processes of cellular metabolism are driven by osmotic pressure, which depends on water channels. Membrane proteins such as aquaporins (AQPs) are…
Plasma chemistry of main air components is implemented in a hybrid 2D axisymmetric simulation code to assess the air-breathing concept in an electrodeless plasma thruster. Relevant electron-heavy species collisions for diatomic molecules…
A macroscopic fluid pump works according to the law of Newtonian mechanics and transfers a large number of molecules per cycle (of the order of 10^23). By contrast, a nano-scale charge pump can be thought as the ultimate miniaturization of…
Nonadiabatic molecular dynamics (NAMD) is widely used to describe hot electron relaxation and nonradiative recombination processes, but high computational costs limit its application to large supercells. Here, we implement a nonadiabatic…
The pump process of the ratchet model inspired by the $F_o$ rotatory motor of ATP synthase is investigated. In this model there are two kinds of characteristic time. One is dynamical, the relaxation time of the system. Others are chemical,…
Simulating the dynamics of molecular excitons in complex nanophotonic environments requires integrating rigorous electromagnetic simulations with accurate treatments of open quantum system dynamics. In this work, we develop MQED-QD…
In recent years, machine learning interatomic potentials (MLIPs) have attracted significant attention as a method that enables large-scale, long-time atomistic simulations while maintaining accuracy comparable to electronic structure…
Large-payload deep space missions are impractical with current rocket propulsion technologies in use. Chemical thrusters yield a high thrust but low efficiency while ion thrusters are efficient but provide too little thrust for large…
The Q-cycle mechanism plays an important role in the conversion of the redox energy into the energy of the proton electrochemical gradient across the biomembrane. The bifurcated electron transfer reaction, which is built into this…
Electrochemical devices often consist of multicomponent electrolyte solutions. Two processes influence the overall dynamics of these devices: the formation of electrical double layers and chemical conversion due to redox reactions. However,…