Related papers: Multi-scale Molecular Simulations on Respiratory C…
Biological functions in each animal cell depend on coordinated operations of a wide variety of molecular motors. Some of the these motors transport cargo to their respective destinations whereas some others are mobile workshops which…
The simulation of electronic systems is an anticipated application for quantum-centric computers, i.e. heterogeneous architectures where classical and quantum processing units operate in concert. An important application is the computation…
Hydrogen recombination is one of the most important atomic processes in many astrophysical objects such as Type II supernova (SN~II) atmospheres, the high redshift universe during the cosmological recombination era, and H II regions in the…
We present the results of experimental and theoretical studies of fast anisotropic relaxation and rotational diffusion in the first electron excited state of biological coenzyme NADH in water-ethanol solutions. The experiments have been…
An adaptive modeling method (AMM) that couples a deep neural network potential and a classical force field is introduced to address the accuracy-efficiency dilemma faced by the molecular simulation community. The AMM simulated system is…
Here, steady-state reaction networks are inspected from the viewpoint of individual tagged molecules jumping among their chemical states upon the occurrence of reactive events. Such an agent-based viewpoint is useful for selectively…
Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this…
The role of rotational molecular motors of the ATP synthase class is integral to the metabolism of cells. Yet the function of FliI6-FliJ complex - homologous to the F1 ATPase motor - within the flagellar export apparatus remains unclear. We…
We analyze the dynamics of rotary biomotors within a simple nano-electromechanical model, consisting of a stator part and a ring-shaped rotor having twelve proton-binding sites. This model is closely related to the membrane-embedded F$_0$…
A cooperative drug delivery system is proposed, where quorum sensing (QS), a density-dependent bacterial behavior coordination mechanism, is employed by synthetic bacterium-based nanomachines (B-NMs) for controllable drug delivery. In our…
Two-component nanoplasmas generated by strong-field ionization of doped helium nanodroplets are studied in a pump-probe experiment using few-cycle laser pulses in combination with molecular dynamics simulations. High yields of helium ions…
A flexible treatment for gas- and aerosol-phase chemical processes has been developed for models of diverse scale, from box models up to global models. At the core of this novel framework is an "abstracted aerosol representation" that…
In recent years there has been significant progress in the development of artificial ion pumping membranes. Ion pumps based on asymmetric nano-pores have been shown to operate as ionic current rectifiers, thus pumping a net ion flux against…
The Improved Quantum Molecular Dynamics (ImQMD) model incorporated with the statistical decay model is successful in describing emission of nucleons in the intermediate energy spallation reactions, but not good enough in describing…
Feedback from AGN jets has been proposed to counteract the catastrophic cooling in many galaxy clusters. However, it is still unclear which physical processes are acting to couple the energy from the bi-directional jets to the ICM. We study…
Correlated many-fermion systems emerge in a broad range of phenomena in warm dense matter, plasmonics, and ultracold atoms. Quantum hydrodynamics (QHD) complements common first-principles methods for many-fermion systems and enables…
A topological charge pump [1] transfers charge in a quantized fashion. The quantization is stable against the detailed form of the pumping protocols and external noises and shares the same topological origin as the quantum Hall effect. We…
We present a multiscale simulation approach for hydroxide transport in aqueous solutions of potassium hydroxide, combining ab initio molecular dynamics (AIMD) simulations with force field ensemble averaging and lattice Monte Carlo…
We present a simulation method that allows us to calculate the titration curves for systems undergoing protonation/deprotonation reactions -- such as charged colloidal suspensions with acidic/basic surface groups, polyelectrolytes,…
We present a theory that efficiently describes the quantum dynamics of an electronic excitation that is coupled to a continuous, highly structured phonon environment. Based on a stochastic approach to non-Markovian open quantum systems, we…