SSAGES : Software Suite for Advanced General Ensemble Simulations

Molecular simulation has emerged as an essential tool for modern-day research, but obtaining proper results and making reliable conclusions from simulations requires adequate sampling of the system under consideration. To this end, a variety of methods exist in the literature that can enhance sampling considerably, and increasingly sophisticated, effective algorithms continue to be developed at a rapid pace. Implementation of these techniques, however, can be challenging for experts and non-experts alike. There is a clear need for software that provides rapid, reliable, and easy access to a wide range of advanced sampling methods and that facilitates implementation of new techniques as they emerge. Here we present SSAGES, a publicly available Software Suite for Advanced General Ensemble Simulations designed to interface with multiple widely used molecular dynamics simulations packages. SSAGES allows facile application of a variety of enhanced sampling techniques—including adaptive biasing force, string methods, and forward flux sampling—that extract meaningful free energy and transition path data from all-atom and coarse-grained simulations. A noteworthy feature of SSAGES is a user-friendly framework that facilitates further development and implementation of new methods and collective variables. In this work, the use of SSAGES is illustrated in the context of simple representative applications involving distinct methods and different collective variables that are available in the current release of the suite. The code may be found at: https://github.com/MICCoM/SSAGES-public

Computational Modeling and Analysis of Insulin Induced Eukaryotic Translation Initiation

Insulin, the primary hormone regulating the level of glucose in the bloodstream, modulates a variety of cellular and enzymatic processes in normal and diseased cells. Insulin signals are processed by a complex network of biochemical interactions which ultimately induce gene expression programs or other processes such as translation initiation. Surprisingly, despite the wealth of literature on insulin signaling, the relative importance of the components linking insulin with translation initiation remains unclear. We addressed this question by developing and interrogating a family of mathematical models of insulin induced translation initiation. The insulin network was modeled using mass-action kinetics within an ordinary differential equation (ODE) framework. A family of model parameters was estimated, starting from an initial best fit parameter set, using 24 experimental data sets taken from literature. The residual between model simulations and each of the experimental constraints were simultaneously minimized using multiobjective optimization. Interrogation of the model population, using sensitivity and robustness analysis, identified an insulin-dependent switch that controlled translation initiation. Our analysis suggested that without insulin, a balance between the pro-initiation activity of the GTP-binding protein Rheb and anti-initiation activity of PTEN controlled basal initiation. On the other hand, in the presence of insulin a combination of PI3K and Rheb activity controlled inducible initiation, where PI3K was only critical in the presence of insulin. Other well known regulatory mechanisms governing insulin action, for example IRS-1 negative feedback, modulated the relative importance of PI3K and Rheb but did not fundamentally change the signal flow

Self Assembly with DNA: From Materials Design to Chromatin

The ability to engineer the self-assembly of nano-scale objects to create highly ordered materials is of considerable scientific and practical interest. This new class of materials represents a powerful approach for engineering a next generation of devices, whose mechanical, optical, and electrical properties can be precisely tuned at the molecular scale. Though significant strides towards this goal have been achieved in recent years, the complexity achieved in engineered systems is still far surpassed by that achieved by nature. Precise self-assembly is achieved by nature through proteins and nucleic acids that fold into intricate, three-dimensional, and importantly, functional structures. A promising avenue towards improved engineered systems is to draw on discoveries from biophysics in order to inspire new approaches and paradigms for self-assembly and materials design. In this work, we explore the interplay between biophysics and engineering by exploring the self-assembly of DNA. Our discussion begins at the smallest length-scales of DNA, first by understanding the hybridization of DNA, and then at how hybridization can be used in materials to direct the self-assembly of gold nanoparticles. We report the first evidence of a tunable mechanical response in these assemblies, thereby suggesting the possibility of mechanical meta-materials constructed using DNA. Our discussion then proceeds to larger length scales, where we examine the biophysical processes that control the compaction of DNA into chromatin. Using a detailed molecular model, we explore the free energies and dynamics of smallest building block of chromatin, a protein-DNA complex called the nucleosome. Our results are in quantitative agreement with existing experimental measurements, and help to explain the molecular factors that dictate the first stages of DNA compaction into chromatin. Lastly, we present a multi-scale approach that can couple information across different length scales of chromatin in order to examine the folding of large regions DNA. By drawing on both the biophysics and engineering literature, the findings presented here suggest new approaches for materials design, and offer new paradigms for synthetic systems that seek to mimic the complexity achieved by nature

Tension-Dependent Free Energies of Nucleosome Unwrapping

Nucleosomes form the basic unit of compaction within eukaryotic genomes and their locations represent an important, yet poorly understood, mechanism of genetic regulation. Quantifying the strength of interactions within the nucleosome is a central problem in biophysics and is critical to understanding how nucleosome positions influence gene expression. By comparing to single-molecule experiments, we demonstrate that a coarse-grained molecular model of the nucleosome can reproduce key aspects of nucleosome unwrapping. Using detailed simulations of DNA and histone proteins, we calculate the tension-dependent free energy surface corresponding to the unwrapping process. The model reproduces quantitatively the forces required to unwrap the nucleosome, and reveals the role played by electrostatic interactions during this process. We then demonstrate that histone modifications and DNA sequence can have significant effects on the energies of nucleosome formation. Most notably, we show that histone tails are crucial for stabilizing the outer turn of nucleosomal DNA.Comment: Submitted for review to PNAS on 4/12/201

Mechanical Response of DNA–Nanoparticle Crystals to Controlled Deformation

The self-assembly of DNA-conjugated nanoparticles represents a promising avenue toward the design of engineered hierarchical materials. By using DNA to encode nanoscale interactions, macroscale crystals can be formed with mechanical properties that can, at least in principle, be tuned. Here we present <i>in silico</i> evidence that the mechanical response of these assemblies can indeed be controlled, and that subtle modifications of the linking DNA sequences can change the Young’s modulus from 97 kPa to 2.1 MPa. We rely on a detailed molecular model to quantify the energetics of DNA–nanoparticle assembly and demonstrate that the mechanical response is governed by entropic, rather than enthalpic, contributions and that the response of the entire network can be estimated from the elastic properties of an individual nanoparticle. The results here provide a first step toward the mechanical characterization of DNA–nanoparticle assemblies, and suggest the possibility of mechanical metamaterials constructed using DNA

Efficient Synthesis of Asymmetric Miktoarm Star Polymers

Asymmetric miktoarm star polymers comprising an unequal number of chemically-distinct blocks connected at a common junction produce unique material properties, yet existing synthetic strategies are beleaguered by complicated reaction schemes that are restricted in both monomer scope and yield. Here, we introduce a new synthetic approach coined "μSTAR" - Miktoarm Synthesis by Termination After Ring-opening metathesis polymerization - that circumvents these traditional synthetic limitations by constructing the block-block junction in a scalable, one-pot process involving (1) grafting-through polymerization of a macromonomer followed by (2) in-situ enyne-mediated termination to install a single mikto-arm with exceptional efficiency. This modular μSTAR platform cleanly generates AB n and A(BA') n miktoarm star polymers with unprecedented versatility in the selection of A and B chemistries as demonstrated using many common polymer building blocks: poly(siloxane), poly(acrylate), poly(methacrylate), poly(ether), poly(ester), and poly(styrene). The average number of B or BA' arms (n) is easily controlled by the molar equivalents of macromonomer relative to Grubbs catalyst in the initial ring-opening metathesis polymerization step. While these materials are characterized by dispersity in n that arises from polymerization statistics, they self-assemble into mesophases that are identical to those predicted for precise miktoarm stars as evidenced by small-angle X-ray scattering experiments and self-consistent field theory simulations. In summary, the μSTAR technique provides a significant boost in design flexibility and synthetic simplicity while retaining the salient phase behavior of precise miktoarm star materials

Stability of the A15 phase in diblock copolymer melts.

The self-assembly of block polymers into well-ordered nanostructures underpins their utility across fundamental and applied polymer science, yet only a handful of equilibrium morphologies are known with the simplest AB-type materials. Here, we report the discovery of the A15 sphere phase in single-component diblock copolymer melts comprising poly(dodecyl acrylate)-block-poly(lactide). A systematic exploration of phase space revealed that A15 forms across a substantial range of minority lactide block volume fractions (f L = 0.25 - 0.33) situated between the σ-sphere phase and hexagonally close-packed cylinders. Self-consistent field theory rationalizes the thermodynamic stability of A15 as a consequence of extreme conformational asymmetry. The experimentally observed A15-disorder phase transition is not captured using mean-field approximations but instead arises due to composition fluctuations as evidenced by fully fluctuating field-theoretic simulations. This combination of experiments and field-theoretic simulations provides rational design rules that can be used to generate unique, polymer-based mesophases through self-assembly