We examined real-time-propagation time-dependent density functional theory (rtp-TDDFT) coupled with molecular dynamics (MD), which uses single-particle representation of time-evolving wavefunctions allowing exchange of orbital characteristics between occupied and empty states making the effective Kohn-Sham Hamiltonian dependent on the potential energy surfaces (PESs). This scheme is expected to lead to mean-field average of adiabatic potential energy surfaces (PESs), and is one of Ehrenfest (mean-field) approaches. However, we demonstrate that the mean-field average can be absent in simulating photoisomerization of azobenzene and ethylene molecules. A transition from the S2 to the S1 excited state without the mean- field average was observed after examining several rtp-TDDFT-MD trajectories of a photoexcited azobenzene molecule. The subsequent trans-cis isomerization was observed in our simulation, which is consistent with experimental observation and supported by previous calculations. The absence of the mean-field average of PESs was also observed for the transition between the S1 and S0 states, indicating that the MD simulation was on a single PES. Conversely, we found no transition to the ground state (S0 state) when we performed a MD simulation of an S1 excited ethylene molecule owing to the constraint on the occupation number of each molecular orbital. Thus, we conclude that, at least for azobenzene and ethylene molecules, the rtp-TDDFT-MD is an on-the-fly simulation that can automatically see the transition among the PESs of excited states without the mean-field average unless the simulation reaches the PES of the S0 state.
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http://dx.doi.org/10.1038/srep18220 | DOI Listing |
Commun Phys
December 2024
Institut für Theoretische Physik, TU Wien, Wiedner Hauptstraße 8-10, A-1040 Wien, Austria.
Despite the intrinsic charge heterogeneity of proteins plays a crucial role in the liquid-liquid phase separation (LLPS) of a broad variety of protein systems, our understanding of the effects of their electrostatic anisotropy is still in its early stages. We approach this issue by means of a coarse-grained model based on a robust mean-field description that extends the DLVO theory to non-uniformly charged particles. We numerically investigate the effect of surface charge patchiness and net particle charge on varying these features independently and with the use of a few parameters only.
View Article and Find Full Text PDFACS Phys Chem Au
November 2024
Department of Physics, Bryn Mawr College, Bryn Mawr, Pennsylvania 19010, United States.
Protein dynamics in the unfolded state, in the context of early stage protein folding or intrinsically disordered proteins (IDPs), is not well understood. The discovery of IDPs, and their sequence-dependent dynamics, has led to many computational and experimental investigations regarding the conformational preferences of short oligopeptides and individual amino acid residues in the unfolded state. As proteins consist of sequences of amino acid residues, characterizing the intrinsic conformational preferences of the individual residues in the unfolded state is crucial for understanding the emergent conformations of peptides and proteins.
View Article and Find Full Text PDFLangmuir
December 2024
School of Materials Science and Engineering, Xi'an University of Technology, Xi'an, Shaanxi 710048, China.
Coarsening is a very common phenomenon that has a crucial impact on the average grain size and properties of materials. However, our current understanding of coarsening is mainly based on the mean-field theories or ex situ observations, and the influence of transient process-related phenomena, such as grain rotation, inverse growth, etc., on coarsening was not considered.
View Article and Find Full Text PDFPhys Rev E
September 2024
Centro Atómico Bariloche and Instituto Balseiro, CNEA, CONICET and Universidad Nacional de Cuyo, 8400 Bariloche, Argentina.
We numerically investigate the geometry and transport properties of infection fronts within the spatial SIR model in two dimensions. The model incorporates short-range correlated quenched random transmission rates. Our findings reveal that the critical average transmission rate for the steady-state propagation of the infection is overestimated by the naive mean-field homogenization.
View Article and Find Full Text PDFPhys Rev E
September 2024
Institut de Biologie de l'ENS, Ecole Normale Supérieure, CNRS, Inserm, Université PSL, 46 rue d'Ulm, 75005 Paris, France.
Nonequilibrium cluster-cluster aggregation of particles diffusing in or at the cell membrane has been hypothesized to lead to domains of finite size in different biological contexts, such as lipid rafts, cell adhesion complexes, or postsynaptic domains in neurons. In this scenario, the desorption of particles balances a continuous flux to the membrane, imposing a cutoff on possible aggregate sizes and giving rise to a stationary size distribution. Here, we investigate the case of nonequilibrium cluster-cluster aggregation in two dimensions where diffusing particles and/or clusters remain fixed in space at specific anchoring sites, which should be particularly relevant for synapses but may also be present in other biological or physical systems.
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