Related papers: Resolving dynamics and function of transient state…
Transferable excited-state dynamics offer a route to efficient screening of photophysical behavior across molecular systems, but conventional nonadiabatic simulations remain prohibitively expensive. Here we introduce X-MACE, a transferable…
A stochastic model for the dynamics of enzymatic catalysis in explicit, effective solvents under physiological conditions is presented. Analytically-computed first passage time densities of a diffusing particle in a spherical shell with…
The transition to a hidden metastable state in 1T-TaS2 is investigated in real time using coherent time-resolved femtosecond spectroscopy. Relying on spectral differences between phonon modes in the equilibrium states and in the metastable…
Although solid helium-4 (4He) may be a supersolid it also exhibits many phenomena unexpected in that context. We studied relaxation dynamics in the resonance frequency f(T) and dissipation D(T) of a torsional oscillator containing solid…
Determining the complete set of ligands' binding/unbinding pathways is important for drug discovery and to rationally interpret mutation data. Here we have developed a metadynamics-based technique that addressed this issue and allows…
Conformational changes of single proteins are monitored in real time by Forster-type resonance energy transfer, FRET. Two different fluorophores have to be attached to those protein domains, which move during function. The distance between…
The tubulin-like protein FtsZ is crucial for cytokinesis in bacteria and many archaea, forming a ring-shaped structure called the Z-ring at the site of cell division. Despite extensive research, the self-assembly of Z-rings is not entirely…
One of the most intriguing results of single molecule experiments on proteins and nucleic acids is the discovery of functional heterogeneity: the observation that complex cellular machines exhibit multiple, biologically active…
Interactions between actin, an anionic polyelectrolyte, and lysozyme, a cationic globular protein, have been examined using a combination of synchrotron small-angle x-ray scattering and molecular dynamics simulations. Lysozyme initially…
We examine a two-dimensional system of sterically repulsive interacting disks where each particle runs in a random direction. This system is equivalent to a run-and-tumble dynamics system in the limit where the run time is infinite. At low…
The high frequency collective dynamics of liquid hydrogen fluoride is studied by inelastic x-ray scattering on the coexistence curve at T = 239 K. The comparison with existing molecular dynamics simulations shows the existence of two active…
(Photo)electrocatalysts capture sunlight and use it to drive chemical reactions such as water splitting to produce H2. A major factor limiting photocatalyst development is their large heterogeneity which spatially modulates reactivity and…
We study the statistics of the fluorescence decay rates for single quantum emitters embedded in a scattering medium undergoing a phase transition. Under certain circumstances, the structural properties of the scattering medium explore a…
We present TTCF4LAMMPS, a toolkit for performing non-equilibrium molecular dynamics (NEMD) simulations to study fluid behaviour at low shear rates using the LAMMPS software. By combining direct NEMD simulations and the transient-time…
Recent demonstrations of extraordinary stabilization of proteins in mobile protic [1] and aprotic [2] ionic liquid solutions at ambient temperatures have raised hopes of new biopreservation and drug transportation technologies. Here we…
We investigate the crystallization of a single, flexible homopolymer chain using transition path sampling (TPS). The chain consists of N identical spherical monomers evolved according to Langevin dynamics. While neighboring monomers are…
Dynamic cooperativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic…
A coarse-grained computational procedure based on the Finite Element Method is proposed to calculate the normal modes and mechanical response of proteins and their supramolecular assemblies. Motivated by the elastic network model, proteins…
A wide variety of feed gases are used to generate low-temperature plasmas for the microelectronics and the sustainability applications. These plasmas often have a complex combination of reactive and non-reactive species which may have…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…