Conformational Dynamics of Bacteriochlorophyll in Chlorosomes from the Mutant of .

In contrast to the common viewpoint that bacteriochlorophyll (BChl) motion is largely absent within the chlorosome assembly, physics-based modeling points to a crucial role of the nanoscale librational motion of the macrocycle for the transfer of excitons. To elucidate this motion experimentally, compositional uniformity and high sensitivity are required. We focused on uniformly C labeled chlorosome preparations from the mutant with significantly enhanced structural homogeneity.

Observation of Dark States in Two-Dimensional Electronic Spectra of Chlorosomes.

Observations of low-lying dark states in several photosynthetic complexes challenge our understanding of the mechanisms behind their efficient energy transfer processes. Computational models are necessary for providing novel insights into the nature and function of dark states, especially since these are not directly accessible in spectroscopy experiments. Here, we will focus on signatures of dark-type states in chlorosomes, a light-harvesting complex from green sulfur bacteria well-known for uniting a broad absorption band with very efficient energy transfer.

An integrated approach towards extracting structural characteristics of chlorosomes from a mutant of .

Chlorosomes, the photosynthetic antenna complexes of green sulfur bacteria, are paradigms for light-harvesting elements in artificial designs, owing to their efficient energy transfer without protein participation. We combined magic angle spinning (MAS) NMR, optical spectroscopy and cryogenic electron microscopy (cryo-EM) to characterize the structure of chlorosomes from a mutant of . The chlorosomes of this mutant have a more uniform composition of bacteriochlorophyll (BChl) with a predominant homolog, [8Ethyl, 12Ethyl] BChl , compared to the wild type (WT).

Analyzing Lipid Membrane Defects via a Coarse-Grained to Triangulated Surface Map: The Role of Lipid Order and Local Curvature in Molecular Binding.

Lipid packing defects are known to serve as quantitative indicators for protein binding to lipid membranes. This paper presents a protocol for mapping molecular lipid detail onto a triangulated continuum leaflet representation. Besides establishing the desired forward counterpart to the existing inverse TS2CG map, this coarse-grained to triangulated surface (CG2TS) map enables straightforward extraction of the defect characteristics for any membrane geometry found in nature.

Covalent Benzenesulfonic Functionalization of a Graphene Nanopore for Enhanced and Selective Proton Transport.

A fundamental understanding of proton transport through graphene nanopores, defects, and vacancies is essential for advancing two-dimensional proton exchange membranes (PEMs). This study employs ReaxFF molecular dynamics, metadynamics, and density functional theory to investigate the enhanced proton transport through a graphene nanopore. Covalently functionalizing the nanopore with a benzenesulfonic group yields consistent improvements in proton permeability, with a lower activation barrier (≈0.

Phase-Separated Lipid-Based Nanoparticles: Selective Behavior at the Nano-Bio Interface.

The membrane-protein interface on lipid-based nanoparticles influences their in vivo behavior. Better understanding may evolve current drug delivery methods toward effective targeted nanomedicine. Previously, the cell-selective accumulation of a liposome formulation in vivo is demonstrated, through the recognition of lipid phase-separation by triglyceride lipases.

Photon Energy-Dependent Ultrafast Exciton Transfer in Chlorosomes of and the Role of Supramolecular Dynamics.

The antenna complex of green sulfur bacteria, the chlorosome, is one of the most efficient supramolecular systems for efficient long-range exciton transfer in nature. Femtosecond transient absorption experiments provide new insight into how vibrationally induced quantum overlap between exciton states supports highly efficient long-range exciton transfer in the chlorosome of . Our work shows that excitation energy is delocalized over the chlorosome in <1 ps at room temperature.

Ultrafast Anisotropy Decay Reveals Structure and Energy Transfer in Supramolecular Aggregates.

Chlorosomes from green bacteria perform the most efficient light capture and energy transfer, as observed among natural light-harvesting antennae. Hence, their unique functional properties inspire developments in artificial light-harvesting and molecular optoelectronics. We examine two distinct organizations of the molecular building blocks as proposed in the literature, demonstrating how these organizations alter light capture and energy transfer, which can serve as a mechanism that the bacteria utilize to adapt to changes in light conditions.

Manifestation of Hydrogen Bonding and Exciton Delocalization on the Absorption and Two-Dimensional Electronic Spectra of Chlorosomes.

Chlorosomes are supramolecular aggregates that contain thousands of bacteriochlorophyll molecules. They perform the most efficient ultrafast excitation energy transfer of all natural light-harvesting complexes. Their broad absorption band optimizes light capture.

A Core-Shell Approach for Systematically Coarsening Nanoparticle-Membrane Interactions: Application to Silver Nanoparticles.

The continuous release of engineered nanomaterial (ENM) into the environment may bring about health concerns following human exposure. One important source of ENMs are silver nanoparticles (NPs) that are extensively used as anti-bacterial additives. The introduction of ENMs into the human body can occur via ingestion, skin uptake or the respiratory system.

Predicted Adsorption Affinity for Enteric Microbial Metabolites to Metal and Carbon Nanomaterials.

Ingested nanomaterials are exposed to many metabolites that are produced, modified, or regulated by members of the enteric microbiota. The adsorption of these metabolites potentially affects the identity, fate, and biodistribution of nanomaterials passing the gastrointestinal tract. Here, we explore these interactions using in silico methods, focusing on a concise overview of 170 unique enteric microbial metabolites which we compiled from the literature.

The role of chirality and plastic crystallinity in the optical and mechanical properties of chlorosomes.

The most efficient light-harvesting antennae found in nature, chlorosomes, are molecular tubular aggregates (TMAs) assembled by pigments without protein scaffolds. Here, we discuss a classification of chlorosomes as a unique tubular plastic crystal and we attribute the robust energy transfer in chlorosomes to this unique nature. To systematically study the role of supramolecular tube chirality by molecular simulation, a role that has remained unresolved, we share a protocol for generating realistic tubes at atomic resolution.

Liposome fusion with orthogonal coiled coil peptides as fusogens: the efficacy of roleplaying peptides.

Biological membrane fusion is a highly specific and coordinated process as a multitude of vesicular fusion events proceed simultaneously in a complex environment with minimal off-target delivery. In this study, we develop a liposomal fusion model system with specific recognition using lipidated derivatives of a set of four designed heterodimeric coiled coil (CC) peptide pairs. Content mixing was only obtained between liposomes functionalized with complementary peptides, demonstrating both fusogenic activity of CC peptides and the specificity of this model system.

Efficient and realistic simulation of phase coexistence.

We show how an existing concurrent multi-scale method named hybrid particle field-molecular dynamics (hPF-MD) can be adapted to enable the simulation of structure and/or structural dynamics in compressible systems. Implementing such new equations of state (EOS) into hPF-MD, while conserving the efficiency associated with treating intermolecular interactions in a continuum fashion, opens this method up to describe a new class of phenomena in which non-uniform densities play a role, for example, evaporation and crystallization. We carefully consider how compressible hPF-MD compares to its mean-field counterpart for two particular EOS, adopted from the Cell Model for polymers and the Carnahan-Starling expression for hard spheres.

Unfolding the prospects of computational (bio)materials modeling.

In this perspective communication, we briefly sketch the current state of computational (bio)material research and discuss possible solutions for the four challenges that have been increasingly identified within this community: (i) the desire to develop a unified framework for testing the consistency of implementation and physical accuracy for newly developed methodologies, (ii) the selection of a standard format that can deal with the diversity of simulation data and at the same time simplifies data storage, data exchange, and data reproduction, (iii) how to deal with the generation, storage, and analysis of massive data, and (iv) the benefits of efficient "core" engines. Expressed viewpoints are the result of discussions between computational stakeholders during a Lorentz center workshop with the prosaic title Workshop on Multi-scale Modeling and are aimed at (i) improving validation, reporting and reproducibility of computational results, (ii) improving data migration between simulation packages and with analysis tools, (iii) popularizing the use of coarse-grained and multi-scale computational tools among non-experts and opening up these modern computational developments to an extended user community.

Dynamic Disorder Drives Exciton Transfer in Tubular Chlorosomal Assemblies.

Chlorosomes stand out for their highly efficient excitation energy transfer (EET) in extreme low light conditions. Yet, little is known about the EET when a chlorosome is excited to a pure state that is an eigenstate of the exciton Hamiltonian. In this work, we consider the dynamic disorder in the intermolecular electronic coupling explicitly by calculating the electronic coupling terms in the Hamiltonian using nuclear coordinates that are taken from molecular dynamics simulation trajectories.

Power generation by reverse electrodialysis in a single-layer nanoporous membrane made from core-rim polycyclic aromatic hydrocarbons.

Nanoporous graphene and related atomically thin layered materials are promising candidates in reverse electrodialysis research owing to their remarkable ionic conductivity and high permselectivity. The synthesis of atomically thin nanoporous membranes with a narrow pore size distribution, however, remains challenging. Here, we report the fabrication of nanoporous carbon membranes via the thermal crosslinking of core-rim structured monomers, that is, polycyclic aromatic hydrocarbons.

Aggregation of Lipid A Variants: A Hybrid Particle-Field Model.

Lipid A is one of the three components of bacterial lipopolysaccharides constituting the outer membrane of Gram-negative bacteria, and is recognized to have an important biological role in the inflammatory response of mammalians. Its biological activity is modulated by the number of acyl-chains that are present in the lipid and by the dielectric medium, i.e.

Contrasting Modes of Self-Assembly and Hydrogen-Bonding Heterogeneity in Chlorosomes of .

Chlorosome antennae form an interesting class of materials for studying the role of structural motifs and dynamics in nonadiabatic energy transfer. They perform robust and highly quantum-efficient transfer of excitonic energy while allowing for compositional variation and completely lacking the usual regulatory proteins. Here, we first cast the geometrical analysis for ideal tubular scaffolding models into a formal framework, to relate effective helical properties of the assembly structures to established characterization data for various types of chlorosomes.

Biomembrane solubilization mechanism by Triton X-100: a computational study of the three stage model.

The solubilization mechanism of lipid membranes in the presence of Triton X-100 (TX-100) is investigated at molecular resolution using molecular dynamics (MD) simulations. Thanks to the large time and length scales accessible by the hybrid particle-field formulation of the models employed here, the complex process of membrane solubilization has been studied, with the goal of verifying the three stage model reported in the literature. DPPC lipid bilayers and vesicles have been studied at different concentrations of the TX-100 detergent employing coarse grained (CG) models.

Combining cell-based hydrodynamics with hybrid particle-field simulations: efficient and realistic simulation of structuring dynamics.

We have extended an existing hybrid MD-SCF simulation technique that employs a coarsening step to enhance the computational efficiency of evaluating non-bonded particle interactions. This technique is conceptually equivalent to the single chain in mean-field (SCMF) method in polymer physics, in the sense that non-bonded interactions are derived from the non-ideal chemical potential in self-consistent field (SCF) theory, after a particle-to-field projection. In contrast to SCMF, however, MD-SCF evolves particle coordinates by the usual Newton's equation of motion.

Erratum. Computational insight in the role of fusogenic lipopeptides at the onset of liposome fusion.

We performed an extensive computational study to obtain insight in the molecular mechanisms that take place prior to membrane fusion. We focused on membrane-anchored hybrid macromolecules (lipid–polymer–oligopeptide) that mimic biological SNARE proteins in terms of liposome fusion characteristics [H. Robson Marsden et al.

Rigorous embedding of cell dynamics simulations in the Cahn-Hilliard-Cook framework: Imposing stability and isotropy.

We have rigorously analyzed the stability of the efficient cell dynamics simulations (CDS) method by making use of the special properties of the local averaging operator 〈〈*〉〉-* in matrix form. Besides resolving a theoretical issue that has puzzled many over the past three decades, this analysis has considerable practical value: It relates CDS directly to finite-difference approximations of the Cahn-Hilliard-Cook equations and provides a straightforward recipe for replacing the original two- or three-dimensional (2D or 3D) averaging operators in CDS by an equivalent (in terms of stability) discrete Laplacian with superior isotropy and scaling behavior. As such, we open up a route to suppress the unphysical reflection of the computational grid in CDS results (grid artifacts).

Computational insight in the role of fusogenic lipopeptides at the onset of liposome fusion.

We performed an extensive computational study to obtain insight in the molecular mechanisms that take place prior to membrane fusion. We focused on membrane-anchored hybrid macromolecules (lipid-polymer-oligopeptide) that mimic biological SNARE proteins in terms of liposome fusion characteristics [H. Robson Marsden et al.