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Critical experimental design issues connecting energy transduction and inheritable information within a protocell are explored and elucidated. The protocell design utilizes a photo-driven energy transducer (a ruthenium complex) to turn…
FoF1-ATP synthase is the enzyme that provides the 'chemical energy currency' adenosine triphosphate, ATP, for living cells. The formation of ATP is accomplished by a stepwise internal rotation of subunits within the enzyme. We monitor…
(Abbreviated) In this paper we report on the development of a multiscale method for simulating complex liquid-liquid systems such as water in contact with oil containing asphaltenes. We consider simulations where water drops covered with…
The transport of excitations governs fundamental properties of matter. Particularly rich physics emerges in the interplay between disorder and environmental noise, even in small systems such as photosynthetic biomolecules.…
We present a large-scale experimental study of quantum-computing-based molecular simulation carried out on IQM's Sirius 24-qubit superconducting processor, utilizing up to 16 operational qubits. The work employs Sample-based Quantum…
Equilibrium and biased MACE accelerated MD simulations in aqueous solutions are performed to investigate the ion capture and transport mechanisms of the {P5W30} Preyssler anion (PA) as the smallest representative member of the extended…
A zero-dimensional (volume-averaged) and a pseudo-one-dimensional (plug-flow) model are developed to investigate atmospheric-pressure plasma jet devices operated with He, He/O$_2$, He/N$_2$ and He/N$_2$/O$_2$ mixtures. The models are…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Molecular modelling and simulation of the surface tension of fluids with force fields is discussed. 29 real fluids are studied, including nitrogen, oxygen, carbon dioxide, carbon monoxide, fluorine, chlorine, bromine, iodine, ethane,…
Large-scale computer simulations of chemical atoms are used in a wide range of applications, including batteries, drugs, and more. However, there is a problem with efficiency as it takes a long time due to the large amount of calculation.…
Respiration in bacteria involves a sequence of energetically-coupled electron and proton transfers creating an electrochemical gradient of protons (a proton-motive force) across the inner bacterial membrane. With a simple kinetic model we…
The sawtooth-free hybrid scenario has been achieved recently in ASDEX Upgrade (AUG) with applied non-inductive current sources and auxiliary heating [A. Burckhart et al 2023 Nucl. Fusion 63 126056]. Control experiments in AUG suggest that…
The molecular energies of chemical systems have been successfully calculated on quantum computers, however, more attention has been paid to the dynamic process of chemical reactions in practical application, especially in catalyst design,…
Large-scale first principles molecular dynamics are crucial for simulating complex processes in chemical, biomedical, and materials sciences. However, the unfavorable time complexity with respect to system sizes leads to prohibitive…
The kinetics of plasma assisted low temperature oxidation of C3H8O2Ar mixtures have been studied in a wide specific deposition energy with the help of nanosecond repetitively pulsed discharge. Two types of nanosecond pulsed plasma sources,…
Here we propose an NPT metadynamics simulation scheme for pressure-induced structural phase transitions, using coordination number and volume as collective variables, and apply it to the reconstructive structural transformation $B1$-$B2$ in…
We study a model of a light-induced proton pump in artificial reaction centers. The model contains a molecular triad with four electron states (i.e., one donor state, two photosensitive group states, and one acceptor state) as well as a…
We propose a four-component molecular model of bitumen. The model includes realistic chemical constituents and introduces a coarse-graining level that suppresses the highest frequency modes. Molecular dynamics simulations of the model are…
Molecular dynamics simulations of myoglobin and aspartate aminotransferase, with explicit solvent, are shown to accurately reproduce the experimentally measured molar volumes. Single amino-acid substitution at VAL39 of aspartate…
Numerous aqueous systems host elements in multiple redox states, with wide ranging implications such as their influence on the formation/dissolution of minerals, water toxicity, and nutrient cycling. To uncover governing mechanisms and…