Many methodologies have been proposed to build reliable and computationally fast coarse-grained potentials. Typically, these force fields rely on the assumption that relevant properties of system under examination can be reproduced using a pairwise decomposition effective forces. In this work it is shown an extension multiscale coarse-graining technique employed parameterize certain class two-body three-body from atomistic configurations. The use explicit potentials greatly improves results...

A variety of coarse-grained (CG) models exists for simulation proteins. An outstanding problem is the construction a CG model with physically accurate conformational energetics rivaling all-atom force fields. In present work, atomistic simulations peptide folding and aggregation equilibria are force-matched using multiscale coarse-graining to develop test interaction potential general utility proteins arbitrary sequence. The reduced representation relies on multiple sites maintain...

The multiscale coarse-graining (MS-CG) method obtains CG interactions from atomistic configurations, as demonstrated previously for a variety of soft matter and biological systems. In this article, recent advances in MS-CG algorithms are described, recently developed computer program MSCGFM calculations is introduced. enhance the efficiency stability computations, these incorporated into program. As result efforts, on large scale systems such peptide proteins can become tractable, numerical...

A solvent-free coarse-grained model for a 1:1 mixed dioleoylphosphatidylcholine (DOPC) and dioleoylphospatidylethanolamine (DOPE) bilayer is developed using the multiscale coarse-graining (MS-CG) approach. B-spline basis functions are implemented instead of original cubic spline in MS-CG method. The new able to dramatically reduce memory requirements increase computational efficiency calculation. Various structural properties from CG simulations compared with their corresponding all-atom...

An iterative coarse-graining method is developed for systematically converting an atomistic force field to a model at lower resolution that able accurately reproduce the distribution functions defined in coarse-grained potential. The starts from multiscale (MS-CG) approach, and it iteratively refines using repeated applications of MS-CG algorithm. It justified on basis matching normal equation, which can be considered discrete form Yvon-Born-Green equation liquid state theory. Numerical...

The potential of mean force (PMF) with respect to coarse-grained (CG) coordinates is often calculated in order study the molecular interactions atomistic dynamics (MD) simulations. multiscale coarse-graining (MS-CG) approach enables computation many-body PMF an system terms CG coordinates, which can be used parameterize models based on all-atom configurations. We demonstrate here that MS-CG method also analyze from MD trajectories via calculations. In addition, calculations at different...

The multiscale coarse-graining (MS-CG) method uses simulation data for an atomistic model of a system to construct coarse-grained (CG) potential the system. CG is variational approximation true mean force degrees freedom retained in model. calculation information about positions and forces data. In principle, resulting MS-CG will be accurate representation if basis set complete enough canonical distribution states well sampled by set. practice, configurations that have very high energy are...

Abstract Background Prediction of B-cell epitopes from antigens is useful to understand the immune basis antibody-antigen recognition, and helpful in vaccine design drug development. Tremendous efforts have been devoted this long-studied problem, however, existing methods at least two common limitations. One that they only favor prediction those with protrusive conformations, but show poor performance dealing planar epitopes. The other limit predict all antigenic residues an antigen as...

It is believed that natural biological membranes contain domains of lipid ordered phase enriched in cholesterol and sphingomyelin. Although the existence these domains, called rafts, still not firmly established for membranes, direct microscopic observations diagrams obtained from study three-component mixtures containing saturated phospholipids, unsaturated demonstrate rafts synthetic membranes. The presence or often ascribed to preferential interactions between example, In this work, we...

Abstract Minus-one ribosomal frameshifting is a translational recoding mechanism widely utilized by many RNA viruses to generate accurate ratios of structural and catalytic proteins. An pseudoknot structure located in the overlapping region gag pro genes Simian Retrovirus type 1 (SRV-1) stimulates frameshifting. However, experimental characterization SRV-1 (un)folding dynamics effect base triple formation lacking. Here, we report results our single-molecule nanomanipulation using optical...

Double-stranded RNA (dsRNA) structures form triplexes and RNA-protein complexes through binding to single-stranded (ssRNA) regions proteins, respectively, for diverse biological functions. Hence, targeting dsRNAs major-groove triplex formation is a promising strategy the development of chemical probes potential therapeutics. Short (e.g., 6-10 mer) chemically-modified Peptide Nucleic Acids (PNAs) have been developed that bind sequence specifically at physiological conditions. For example, PNA...

Coarse-grained models designed for intrinsically disordered proteins and regions (IDP/Rs) usually omit some bonded potentials (e.g., angular dihedral potentials) as a conventional strategy to enhance backbone flexibility. However, notable drawback of this approach is the generation inaccurate conformations. Here, we addressed problem by introducing residue-specific angular, refined dihedral, correction map (CMAP) potentials, derived based on statistics from customized coil database. These...

We performed molecular dynamics simulations to study the interactions between model hydrophilic plates made of carbon atoms distributed on a hexagonal lattice. Although neutral, carry equal amounts positive and negative charges represent physical dipoles. Using thermodynamic perturbation theory we calculated potential mean force (PMF) acting as function distance these plates. observed that, at distances when more than one water layer can be found plates, contribution into PMF either...

In this communication we report on molecular dynamics computer simulations of self-assembly reverse micelles in supercritical carbon dioxide. The contain perfluoropolyether ammonium carboxylate surfactants and an aqueous core. We observed a quick these over time periods approximately 5 ns, irrespective initial conditions. most cases, the self-assembled perfluorinated have nice spherical shape properties consistent with experiments. When fluorinated surfactant is replaced by its hydrogenated...

Structure modelling via small-angle X-ray scattering (SAXS) data generally requires intensive computations of intensity from any given biomolecular structure, where the accurate evaluation SAXS profiles using coarse-grained (CG) methods is vital to improve computational efficiency. To date, most CG computing have been based on a single-bead-per-residue approximation but neglected structural correlations between amino acids. accuracy calculations, form factors acids are now derived rigorous...

Candida albicans is a dimorphic fungus that converts from yeast form to hyphae during infection. This switch requires the formation of actin cable coordinate polarized cell growth. It's known nucleation this multiprotein complex localized at tip called polarisome, but mechanisms underpinning process were unclear. Here, we found C. Aip5, homolog polarisome component ScAip5 in Saccharomyces cerevisiae nucleates polymerization and synergizes with formin ScBni1, regulates assembly growth...

Although bactericidal activities of nanomaterials against environmental bacteria have been extensively studied, little is known about the sublethal impacts nanomaterials, which a critical gap in our comprehensive understanding on microbial ecosystems. Using Pseudomonas aeruginosa as model organism, we report for first time that level single-wall carbon nanotubes (SWCNTs) (40 or 80 μg/mL) inhibited production pyoverdine, an important metabolite involved interactive behavior communities....

This paper addresses the problem of robust H 2 and ∞ control discrete linear time-invariant (LTI) systems with polytopic uncertainties via dynamic output feedback. The has been known to be difficult when a parameter dependent Lyapunov function is applied for less conservative design due non-convexity. Our approach based on novel bounding technique that converts non-convex optimization into convex one together line search, which simple but may conservative. To further reduce conservatism, an...

Solvent free models for aqueous ionic solutions are derived using the multiscale coarse-graining (MS-CG) method to obtain many-body potentials of mean force and generalized Langevin equations propagate model in time. The resulting compared other implicit solvent NaCl terms both sampling efficiency accuracy. First, equilibrium structural properties compared, then temperature dependence interion determined pairwise entropy associated with effective interactions. After validating behavior new...

A computational method called the progressive fluctuation matching (PFM) is developed for constructing robust heterogeneous anisotropic network models (HANMs) biomolecular systems. An HANM derived through PFM approach consists of harmonic springs with realistic positive force constants, and yields calculated B-factors that are basically identical to experimental ones. For four tested protein systems including crambin, trypsin inhibitor, HIV-1 protease, lysozyme, root-mean-square deviations...