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We report on a molecular simulation method which captures the self-assembly of cationic lipid-DNA (CL-DNA) gene delivery complexes. Computational efficiency required for large length- and time-scale simulations is achieved through a…
We investigate molecular evolution from a molecular cloud core to a first hydrostatic core in three spatial dimensions. We perform a radiation hydrodynamic simulation in order to trace fluid parcels, in which molecular evolution is…
Bacterial chromosome replication occurs in the absence of a canonical spindle apparatus; yet it reliably produces organised and segregated genomes. While both passive and active mechanisms have been investigated, DNA replication itself is a…
We consider a Markovian model for the kinetics of RNA Polymerase (RNAP) which provides a physical explanation for the phenomenon of cooperative pushing during transcription elongation observed in biochemical experiments on Escherichia coli…
We present a method to simulate ultrafast pump-probe time-resolved circular dichroism (TRCD) spectra based on time-dependent density functional theory trajectory surface hopping. The method is applied to simulate the TRCD spectrum along the…
Designing metal-organic frameworks (MOFs) synthesis protocols is currently largely driven by trial-and-error, since we lack fundamental understanding of the molecular level mechanisms that underlie their self-assembly processes. Previous…
The design of artificial microswimmers is often inspired by the strategies of natural microorganisms. Many of these creatures exploit the fact that elasticity breaks the time-reversal symmetry of motion at low Reynolds numbers, but this…
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…
Oxygen migration in tantalum oxide, a promising next-generation storage material, is studied using in-operando x-ray absorption spectromicroscopy and is used to microphysically describe accelerated evolution of conduction channel and device…
Solute-intercalation-induced phase separation creates spatial heterogeneities in host materials, a phenomenon ubiquitous in batteries, hydrogen storage, and other energy devices. Despite many efforts, probing intercalation processes at the…
Mean-field frozen percolation is a random graph-valued process, which adjusts the dynamics of the classical Erdos-Renyi process with an additional mechanism to 'freeze' potential giant components before they can form. It is known to exhibit…
Cytoskeletal filaments are capable of self-assembly in the absence of externally supplied chemical energy, but the rapid turnover rates essential for their biological function require a constant flux of ATP or GTP hydrolysis. The same is…
Serpentinization and carbonation of ultramafic formations is a ubiquitous phenomenon, which deeply influences the biogeochemical cycles of water, hydrogen, carbon... while supporting the particular biosphere around the oceanic hydrothermal…
Using a high-sensitivity torsional oscillator technique, we mapped the rotational and relaxational dynamics of solid helium-4 throughout the parameter range of the proposed supersolidity. We found evidence that the same microscopic…
The present work continues studies of the mathematical model of a metabolic process of the Krebs cycle. We study the dependence of its cyclicity on the cell respiration intensity determined by the formation level of carbon dioxide. We…
This paper formalizes a widely used dynamical class--replicator-mutator dynamics and Price-style selection-and-transmission--and makes explicit the modeling choices (scale, atomic unit, interaction topology, transmission kernel) that…
DNA helicases are molecular motors that use the energy from ATP hydrolysis to move along DNA, promoting the unwinding or rewinding of the double helix. Here, we use magnetic and optical tweezers to track the motion of three helicases, gp41,…
Computational prediction of RNA structures is an important problem in computational structural biology. Studies of RNA structure formation often assume that the process starts from a fully synthesized sequence. Experimental evidence,…
Solar dynamics and turbulence occur at all heights of the solar atmosphere and could be described as stochastic processes. We propose that finite lifetime transients recurring at a certain place could trigger quasi-periodic processes in the…
The iron thiolate complex is a simplified model of the active site of diiron hydrogenase enzymes. Here, we describe the implementation of this noble metal free catalyst in aqueous solutions using eosin Y as photosensitizer and triethylamine…