Unfolding the prospects of computational (bio)materials modeling

Optimization of parallel implementation of UNRES package for coarse-grained simulations to treat large proteins

We report major algorithmic improvements of the UNRES package for physics-based coarse-grained simulations of proteins. These include (i) introduction of interaction lists to optimize computations, (ii) transforming the inertia matrix to a pentadiagonal form to reduce computing and memory requirements, (iii) removing explicit angles and dihedral angles from energy expressions and recoding the most time-consuming energy/force terms to minimize the number of operations and to improve numerical stability, (iv) using OpenMP to parallelize those sections of the code for which distributed-memory parallelization involves unfavorable computing/communication time ratio, and (v) careful memory management to minimize simultaneous access of distant memory sections. The new code enables us to run molecular dynamics simulations of protein systems with size exceeding 100,000 amino-acid residues, reaching over 1 ns/day (1 μs/day in all-atom timescale) with 24 cores for proteins of this size. Parallel performance of the code and comparison of its performance with that of AMBER, GROMACS and MARTINI 3 is presented.

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. Therefore, evaluating how NPs translocate over bio-membranes is essential in assessing their primary toxicity. Unfortunately, data regarding membrane-NP interaction is still scarce, as is theoretical and in silico insight into what governs adhesion and translocation for the most relevant NPs and membranes. Coarse-grained (CG) molecular descriptions have the potential to alleviate this situation, but are hampered by the absence of a direct link to NP materials and membrane adhesion mechanisms. Here, we interrogate the relationship between the most common NP representation at the CG level and the adhesion characteristics of a model lung membrane. We find that this representation for silver NPs is non-transferable, meaning that a proper CG representation for one size is not suited for other sizes. We also identify two basic types of primary adhesion-(partial) NPs wrapping by the membrane and NP insertion into the membrane-that closely relate to the overall NP hydrophobicity and significantly differ in terms of lipid coatings. The proven non-transferability of the standard CG representation with size forms an inspiration for introducing a core-shell model even for bare NPs that are uniform in composition. Using existing all-atom molecular dynamics (MD) data as a reference, we show that this extension does allow us to reproduce size-dependent NP adhesion properties and lipid responses to NP binding at the CG level. The subsequent CGMD evaluation for 10 nm Ag NPs provides new insight into membrane binding for relevant NP sizes and into the role of water in trapping NPs into defected mixed monolayer-bilayer states. This development will be instrumental for simulating NP-membrane adhesion towards more experimentally relevant length and time scales for particular NP materials.

Path Integral Molecular Dynamics of Liquid Water in a Mean-Field Particle Reservoir

We present a simulation scheme for path integral simulation of molecular liquids where a small open region is embedded in a large reservoir of non interacting point‐particles. The scheme is based on the latest development of the adaptive resolution technique AdResS and allows for the space‐dependent change of molecular resolution from a path integral representation with 120 degrees of freedom to a point particle that does not interact with other molecules and vice versa. The method is applied to liquid water and implies a sizable gain regarding the request of computational resources compared to full path integral simulations. Given the role of water as universal solvent with a specific hydrogen bonding network, the path integral treatment of water molecules is important to describe the quantum effects of hydrogen atoms’ delocalization in space on the hydrogen bonding network. The method presented here implies feasible computational efforts compared to full path integral simulations of liquid water which, on large scales, are often prohibitive.

Mean-field theory of the interaction of the magnesium ion with biopolymers: the case of lysozyme

A statistical theory is presented of the magnesium ion interacting with lysozyme under conditions where the latter is positively charged. Temporarily assuming magnesium is not noncovalently bound to the protein, I solve the nonlinear Poisson-Boltzmann equation accurately and uniformly in a perturbative fashion. The resulting expression for the effective charge, which is larger than nominal owing to overshooting, is subtle and cannot be asymptotically expanded at high ionic strengths that are practical. An adhesive potential taken from earlier work together with the assumption of possibly bound magnesium is then fitted to be in accord with measurements of the second virial coefficient by Tessier et al. The resulting numbers of bound magnesium ions as a function of MgBr[Formula: see text] concentration are entirely reasonable compared with densitometry measurements.

Non-disruptive uptake of anionic and cationic gold nanoparticles in neutral zwitterionic membranes

The potential toxicity of ligand-protected nanoparticles (NPs) on biological targets is crucial for their clinical translation. A number of studies are aimed at investigating the molecular mechanisms shaping the interactions between synthetic NPs and neutral plasma membranes. The role played by the NP surface charge is still widely debated. We compare, via liposome leakage assays, the perturbation induced by the penetration of sub-6 nm anionic and cationic Au NPs into model neutral lipid membranes composed of the zwitterionic 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC). Our charged Au NPs are functionalized by a mixture of the apolar 1-octanethiol and a ω-charged thiol which is either the anionic 11-mercapto-1-undecanesulfonate or the cationic (11-mercaptoundecyl)-N,N,N-trimethylammonium. In both cases, the NP uptake in the bilayer is confirmed by quartz crystal microbalance investigations. Our leakage assays show that both negatively and positively charged Au NPs do not induce significant membrane damage on POPC liposomes when penetrating into the bilayer. By means of molecular dynamics simulations, we show that the energy barrier for membrane penetration is the same for both NPs. These results suggest that the sign of the NP surface charge, per se, does not imply different physicochemical mechanisms of interaction with zwitterionic lipid membranes.