Processes In Condensed Matter Research Articles

Interplay of Mechanochemistry and Material Processes in the Graphite to Diamond Phase Transformation.

The manifestation of intramolecular strains in covalent systems is widely known to accelerate chemical reactions and open alternative reaction paths. This process is moderately well understood for isolated molecules and unimolecular processes. However, in condensed matter processes such as phase transformations, material properties and structure may influence typical mechanochemical effects. Therefore, we utilize steered molecular dynamics to induce out of plane strains in graphite and compress the system under a constant strain rate to induce phase transformation. We show that the out of plane strain allows phase transformations to initiate at small amounts of compressive strain. However, in contrast to typical mechanochemical results, the sum of compressive and out of plane work needed to form a diamond has a local minimum due to altered defect formation processes during phase transformation. Additionally, these altered processes slow the kinetics of the phase transformation, taking longer from initiation to total material transformation.

Stochastic Resonance in Protein Folding Dynamics.

Although protein folding reactions are usually studied under static external conditions, it is likely that proteins fold in a locally fluctuating cellular environment in vivo. To mimic such behavior in in vitro experiments, the local temperature of the solvent can be modulated either harmonically or using correlated noise. In this study, coarse-grained molecular simulations are used to investigate these possibilities, and it is found that both periodic and correlated random fluctuations of the environment can indeed accelerate folding kinetics if the characteristic frequencies of the applied fluctuations are commensurate with the internal timescale of the folding reaction; this is consistent with the phenomenon of stochastic resonance observed in many other condensed-matter processes. To test this theoretical prediction, the folding dynamics of phosphoglycerate kinase under harmonic temperature fluctuations are experimentally probed using Förster resonance energy transfer fluorescence measurements. To analyze these experiments, a combination of theoretical approaches is developed, including stochastic simulations of folding kinetics and an analytical mean-field kinetic theory. The experimental observations are consistent with the theoretical predictions of stochastic resonance in phosphoglycerate kinase folding. When combined with an alternative experiment on the protein VlsE using a power spectrum analysis, elaborated in Dave et al., ChemPhysChem 2016, 10.1002/cphc.201501041, the overall data overwhelmingly point to the experimental confirmation of stochastic resonance in protein folding dynamics.

Simulating open quantum dynamics with time-dependent variational matrix product states: Towards microscopic correlation of environment dynamics and reduced system evolution

Many-body approaches to open quantum systems have recently become powerful tools for investigating the detailed role of dissipative environments in diverse non-equilibrium molecular and condensed matter processes. Here, we report the development of an efficient algorithm that utilises a time-dependent variational principle for matrix product states to evolve large system-environment states. By thus capturing all system-environment correlations, we reproduce the highly non-perturbative, quantum-critical dynamics of the zero temperature spin-boson model, and then exploit the many-body information to output a complete time-frequency spectrum of the environmental excitations. We highlight how theoretical 'environmental spectra' could yield valuable insights into a wide range of complex dissipative processes, by showing that correlated motion of modes entangled with the spin can appear with persistent vibrational coherence, in spite of incoherent spin relaxation.