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The carbonic anhydrase II enzyme (CA II) is one of the most significant enzymes in nature, reversibly converting CO$_2$ to bicarbonate at a remarkable rate. The precise mechanism it uses to achieve this rapid turnover remains unclear due to…
Solid-state electro-aerodynamic propulsion systems are devices that utilize atmospheric pressure corona discharge and have been actively researched in recent years as a means of achieving silent drones. However, these systems contain…
The accurate description of large molecular systems in complex environments remains an ongoing challenge for the field of computational chemistry. This problem is even more pronounced for photo-induced processes, as multiple excited…
The solid acids CsH$_2$PO$_4$ and Cs$_7$(H$_4$PO$_4$)(H$_2$PO$_4$)$_8$ pose significant challenges for the simulation of proton transport phenomena. In this work, we use the recently developed machine-learned force field (MLFF) MACE to…
The transport of excess protons and hydroxide ions in water underlies numerous important chemical and biological processes. Accurately simulating the associated transport mechanisms ideally requires utilizing ab initio molecular dynamics…
We examine charge transport through a system of three sites connected in series in the situation when an oscillating charged piston modulates the energy of the middle site. We show that with an appropriate set of parameters, charge can be…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
The primary target of this paper is to present novel compounds in view of their possible use as oxidizers in propulsion applications using molecular modeling calculations and supersonic flow simulations. Carbon-based heterocyclic compounds…
Mitochondrial adenine nucleotide (AdN) content is regulated through the Ca2+-activated, electroneutral ATP-Mg/Pi carrier (APC). The APC is a protein in the mitochondrial carrier super family that localizes to the inner mitochondrial…
Nano-scale fluid transport has vast applications spanning from water desalination to biotechnology [1,2]. It is possible to pump fluids in nano-conduits using pressure gradients [3], thermal methods [4], electric [5,6] and magnetic fields…
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. Briefly, proton…
This study employed an artificial intelligence-enhanced molecular simulation framework to enable efficient Path Integral Molecular Dynamics (PIMD) simulations. Owing to its modular architecture and high-throughput capabilities, the…
The most important factor for quantitative results in molecular dynamics simulation are well developed force fields and models. In the present work, the development of new models and the usage of force fields from the literature in large…
Manganese(II) mobilised by mining activity poses a persistent water-quality challenge, yet the mechanisms by which low-cost sorbents, such as biochar, sequester Mn(II) remain poorly resolved. This study identifies the specific chemical…
We have developed molecular dynamics codes for a short-range interaction potential that adopt both the flat-MPI and MPI/OpenMP hybrid parallelizations on the basis of a full domain decomposition strategy. Benchmark simulations involving up…
We study ionic liquids composed 1-alkyl-3-methylimidazolium cations and bis(trifluoromethyl-sulfonyl)imide anions ([C$_n$MIm][NTf$_2$]) with varying chain-length $n\!=\!2, 4, 6, 8$ by using molecular dynamics simulations. We show that a…
Controlled charge pumping in an AlGaAs/GaAs gated nanowire by single-parameter modulation is studied experimentally and theoretically. Transfer of integral multiples of the elementary charge per modulation cycle is clearly demonstrated. A…
This paper reviews Irradiation Driven Molecular Dynamics (IDMD) - a novel computational methodology for atomistic simulations of the irradiation driven transformations of complex molecular systems implemented in the MBN Explorer software…
Efficient computational methods that are capable of supporting experimental measures obtained at constant values of pH and redox potential are important tools as they serve to, among other things, provide additional atomic level information…
We analyze one of the simplest active suspensions with complex dynamics: a suspension of immotile "Extensor" particles that exert active extensile dipolar stresses on the fluid in which they are immersed. This is relevant to several…