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F$_{1}$-ATPase is a rotary molecular motor that \emph{in vivo} is subject to strong nonequilibrium driving forces. There is great interest in understanding the operational principles governing its high efficiency of free-energy…
Isothermal-isobaric molecular dynamics simulations are used to examine the microscopic structure and some properties of water-methanol liquid mixture. The TIP4P/2005 and SPC/E water models are combined with the united atom TraPPE and the…
Application of the nonadiabatic molecular dynamics (NAMD) approach is severely limited to studying carrier dynamics in the momentum space, since a supercell is required to sample the phonon excitation and electron-phonon (e-ph) interaction…
Multicomponent lipid mixtures exhibit complex phase behavior, including coexistence of nanoscopic fluid phases in ternary mixtures mimicking the composition of the outer leaflet of mammalian plasma membrane. The physical mechanisms…
Catalytic engines can use hydrogen peroxide as a chemical fuel in order to drive motion at the microscale. The chemo-mechanical actuation is a complex mechanism based on the interrelation between catalytic reactions and…
Quenching of gluonic jets and heavy quark production in Au+Au collisions at RHIC can be understood within the pQCD based 3+1 dimensional parton transport model BAMPS including pQCD bremsstrahlung $2 \leftrightarrow 3$ processes.…
The Anaerobic Digestion Model No. 1 (ADM1) is a complex model which is widely accepted as a common platform for anaerobic process modeling and simulation. However, it has a large number of parameters and states that hinder its analytical…
Aqueous proton transport plays a key role in acid-base neutralization, and energy transport through biological membranes and hydrogen fuel cells. Extensive experimental and theoretical studies have resulted in a highly detailed elucidation…
Accurate simulation of dynamical processes in molecules and reactions is among the most challenging problems in quantum chemistry. Quantum computers promise efficient chemical simulation, but the existing quantum algorithms require many…
Room temperature, wavelength non-degenerate ultrafast pump/probe measurements were performed on GaN and InGaN epilayers and an InGaN multiple quantum well structure. Carrier relaxation dynamics were investigated as a function of excitation…
Quantum chemical calculations on atomistic systems have evolved into a standard approach to study molecular matter. These calculations often involve a significant amount of manual input and expertise although most of this effort could be…
The catalytic conversion ATP + AMP -> 2ADP by the enzyme adenylate kinase (ADK) involves the binding of one ATP molecule to the LID domain and one AMP molecule to the NMP domain. The latter is followed by a phosphate transfer, and then the…
Site-specific information on how adenosine triphosphate in the aqueous phase (ATP$_{(aq)}$) interacts with magnesium (Mg$^{2+}_{(aq)}$) is a prerequisite to understanding its complex biochemistry. To gather such information, we apply…
The essential biological processes that sustain life are catalyzed by protein nano-engines, which maintain living systems in far-from-equilibrium ordered states. To investigate energetic processes in proteins, we have analyzed the system of…
F$_\mathrm{o}$F$_1$-ATP synthase is a factory for synthesizing ATP in virtually all cells. Its core machinery is the subcomplex F$_1$-motor (F$_1$-ATPase) and performs the reversible mechanochemical coupling. Isolated F$_1$-motor hydrolyzes…
The amplitude and probability of quantum transitions are represented as a path integrals in energy state space of the investigated multi-level quantum system. Using this approach we consider rotational dynamics of nitrogen molecules…
Atmospheric aerosol nucleation contributes to more than half of cloud condensation nuclei globally. The emissions, properties and concentrations of atmospheric aerosols or aerosol precursors could respond significantly to climate change.…
Multi-component metal nanoparticles (NPs) are of paramount importance in the chemical industry, as most processes therein employ heterogeneous catalysts. While these multi-component systems have been shown to result in higher product…
Open quantum system approaches are widely used in the description of physical, chemical and biological systems. A famous example is electronic excitation transfer in the initial stage of photosynthesis, where harvested energy is transferred…
Proton transport (PT) in bulk liquid water and within a thin water-filled carbon nanotube has been examined with ab initio pathintegral molecular dynamics (PIMD). Barrierless proton transfer is observed in each case when quantum nuclear…