Nonadiabatic molecular dynamics simulation: An approach based on quantum measurement picture

Mixed-quantum-classical molecular dynamics simulation implies an effective measurement on the electronic states owing to continuously tracking the atomic forces.Based on this insight, we propose a quantum trajectory mean-field approach for nonadiabatic molecular dynamics simulations. The new protocol provides a natural interface between the separate quantum and classical treatments, without invoking artificial surface hopping algorithm. Moreover, it also bridges two widely adopted nonadiabatic dynamics methods, the Ehrenfest mean-field theory and the trajectory surface-hopping method. Excellent agreement with the exact results is illustrated with representative model systems, including the challenging ones for traditional methods

Effects of Antimicrobial Peptide Revealed by Simulations: Translocation, Pore Formation, Membrane Corrugation and Euler Buckling

We explore the effects of the peripheral and transmembrane antimicrobial peptides on the lipid bilayer membrane by using the coarse grained Dissipative Particle Dynamics simulations. We study peptide/lipid membrane complexes by considering peptides with various structure, hydrophobicity and peptide/lipid interaction strength. The role of lipid/water interaction is also discussed. We discuss a rich variety of membrane morphological changes induced by peptides, such as pore formation, membrane corrugation and Euler buckling

Exciton-Phonon Interaction Model for Singlet Fission in Prototypical Molecular Crystals

In singlet fission (SF), a spin-conserving splitting of one singlet exciton into two triplet excitation states, the transition between localized electronic states can be controlled and modulated by delocalized lattice phonons. In this work, we built an exciton–phonon (ex–ph) interaction model accounting local electronic states coupled with both local molecular vibrations and low frequency intermolecular phonon modes for SF in crystalline tetracene and rubrene. On the basis of the calculated electronic couplings at the equilibrium structure of the molecular dimer, a superexchange path for SF was found for tetracene while couplings between the triplet pair (TT) state and other diabatic states are zero for rubrene due to the high symmetry. Our further ex–ph spectral density analysis and quantum dynamics simulation based on our ex–ph interaction model suggested a thermal-activated mechanism for SF in rubrene crystal via symmetry breaking by nuclear vibration, which is in agreement with recent experiments. It is also shown that thermal fluctuations of electronic couplings in both tetracene and rubrene are mostly in the same order of magnitude at room temperature, and this could be one of the reasons for both tetracene and rubrene to exhibit SF time scales within a close range (hundreds to thousands of femtoseconds) in experiments

Dynamics of Oxygen-Independent Photocleavage of Blebbistatin as a One-Photon Blue or Two-Photon Near-Infrared Light-Gated Hydroxyl Radical Photocage

Development of versatile, chemically tunable photocages for photoactivated chemotherapy (PACT) represents an excellent opportunity to address the technical drawbacks of conventional photodynamic therapy (PDT) whose oxygen-dependent nature renders it inadequate in certain therapy contexts such as hypoxic tumors. As an alternative to PDT, oxygen free mechanisms to generate cytotoxic reactive oxygen species (ROS) by visible light cleavable photocages are in demand. Here, we report the detailed mechanisms by which the small molecule blebbistatin acts as a one-photon blue light-gated or two-photon near-infrared light-gated photocage to directly release a hydroxyl radical (•OH) in the absence of oxygen. By using femtosecond transient absorption spectroscopy and chemoselective ROS fluorescent probes, we analyze the dynamics and fate of blebbistatin during photolysis under blue light. Water-dependent photochemistry reveals a critical process of water-assisted protonation and excited state intramolecular proton transfer (ESIPT) that drives the formation of short-lived intermediates, which surprisingly culminates in the release of •OH but not superoxide or singlet oxygen from blebbistatin. CASPT2//CASSCF calculations confirm that hydrogen bonding between water and blebbistatin underpins this process. We further determine that blue light enables blebbistatin to induce mitochondria-dependent apoptosis, an attribute conducive to PACT development. Our work demonstrates blebbistatin as a controllable photocage for •OH generation and provides insight into the potential development of novel PACT agents

Implicit-solvent dissipative particle dynamics force field based on a four-to-one coarse-grained mapping scheme.

A new set of efficient solvent-free dissipative particle dynamics (DPD) force fields was developed for phospholipids and peptides. To enhance transferability, this model maps around four heavy atoms and their connected hydrogen atoms into a coarse-grained elementary bead based on functional group. The effective hybrid potential between any pair of beads is composed of a short-range repulsive soft-core potential that directly adopts the form of an explicit-solvent DPD model and a long-range attractive hydrophobic potential. The parameters of the attractive potentials for lipid molecules were obtained by fitting the explicit-solvent DPD simulation of one bead of any type in a water box, then finely tuning it until the bilayer membrane properties obtained in the explicit-solvent model were matched. These parameters were further extended to amino acids according to bead type. The structural and elastic properties of bilayer membranes, free energy profiles for a lipid flip-flop and amino acid analogues translocating across the membrane, and membrane pore formation induced by antimicrobial peptides obtained from this solvent-free DPD force field considerably agreed with the explicit-solvent DPD results. Importantly, the efficiency of this method is guaranteed to accelerate the assembly of vesicles composed of several thousand lipids by up to 50-fold, rendering the experimental liposome dynamics as well as membrane-peptide interactions feasible at accessible computational expense

Dissipative Particle Dynamics Simulations for Phospholipid Membranes Based on a Four-To-One Coarse-Grained Mapping Scheme.

In this article, a new set of parameters compatible with the dissipative particle dynamics (DPD) force field is developed for phospholipids. The coarse-grained (CG) models of these molecules are constructed by mapping four heavy atoms and their attached hydrogen atoms to one bead. The beads are divided into types distinguished by charge type, polarizability, and hydrogen-bonding capacity. First, we derive the relationship between the DPD repulsive force and Flory-Huggins χ-parameters based on this four-to-one CG mapping scheme. Then, we optimize the DPD force parameters for phospholipids. The feasibility of this model is demonstrated by simulating the structural and thermodynamic properties of lipid bilayer membranes, including the membrane thickness, the area per lipid, the lipid tail orientation, the bending rigidity, the rupture behavior, and the potential of mean force for lipid flip-flop

Structural properties of phospholipids bilayers: membrane thickness <i>L</i>_<i>mem</i>, area per lipid <i>a</i>₀, and orientation order of the hydrocarbon chain <i>S</i>_<i>chain</i> as well as elastic properties: bending rigidity <i>κ</i> and rupture tension Σ_<i>r</i>.

<p>Structural properties of phospholipids bilayers: membrane thickness <i>L</i>_<i>mem</i>, area per lipid <i>a</i>₀, and orientation order of the hydrocarbon chain <i>S</i>_<i>chain</i> as well as elastic properties: bending rigidity <i>κ</i> and rupture tension Σ_<i>r</i>.</p

CG mappings for 20 amino acid residues.

<p>CG mappings for 20 amino acid residues.</p

DPD force parameters <i>a</i>_<i>ij</i> (<i>k</i>_<i>B</i><i>T</i>/<i>r</i>₀).

<p>DPD force parameters <i>a</i>_<i>ij</i> (<i>k</i>_<i>B</i><i>T</i>/<i>r</i>₀).</p

Atomic representation of DMPC lipid and its corresponding CG model.

<p>(A): Inverted Y-shape model by Groot and Rabone [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154568#pone.0154568.ref010" target="_blank">10</a>]. (B): Modified inverted Y-shape model by Kranenburg, Nicolas and Smit [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154568#pone.0154568.ref023" target="_blank">23</a>]. (C): <i>λ</i>-shape model by Shillcock and Lipowsky [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154568#pone.0154568.ref012" target="_blank">12</a>]. (D): h-shape MARTINI model used by us [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154568#pone.0154568.ref031" target="_blank">31</a>–<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0154568#pone.0154568.ref033" target="_blank">33</a>].</p