Phase-separated biomolecular condensates exhibit a wide range of dynamic properties, which depend on the sequences constituent proteins and RNAs. However, it is unclear to what extent condensate dynamics can be tuned without also changing thermodynamic properties that govern phase separation. Using coarse-grained simulations intrinsically disordered proteins, we show thermodynamics homopolymer are strongly correlated, with increased stability being coincident low mobilities high viscosities....

Optimizing force-field (FF) parameters to perform molecular dynamics (MD) simulations is a challenging and time-consuming process. We present novel FF optimization framework that integrates MD with particle swarm (PSO) algorithm artificial neural network (ANN). This new ANN-assisted PSO was used develop transferable coarse-grained (CG) models for D2O DMF as proof of concept. The generate the set input CG these solvents, which were optimized reproduce their experimental properties. Herein,...

Four different machine learning (ML) regression models: artificial neural network, k-nearest neighbors, Gaussian process and random forest were built to backmap coarse-grained models all-atom models. The ML showed better predictions than the existing backmapping approaches for selected structures, suggesting applications of backmapping.

We present a computational framework that integrates coarse-grained (CG) molecular dynamics (MD) simulations and data-driven machine-learning (ML) method to gain insights into the conformations of polymers in solutions. employ this study conformational transition model thermosensitive polymer, poly(N-isopropylacrylamide) (PNIPAM). Here, we have developed first its kind, temperature-independent CG PNIPAM can accurately predict experimental lower critical solution temperature (LCST) while...

We have employed two-to-one mapping scheme to develop three coarse-grained (CG) water models, namely, 1-, 2-, and 3-site CG models. Here, for the first time, particle swarm optimization (PSO) gradient descent methods were coupled optimize force-field parameters of models reproduce density, self-diffusion coefficient, dielectric constant real at 300 K. The MD simulations these new conducted with various timesteps, different system sizes, a range temperatures are able predict constant, surface...

Accurate, faster, and on-the-fly analysis of the molecular dynamics (MD) simulations trajectory becomes very critical during discovery new materials or while developing force-field parameters due to automated nature these processes. Here overcome drawbacks algorithm based approaches, we have developed utilized an approach that integrates machine-learning (ML) stacked ensemble model (SEM) with MD simulations, for first time. As a proof-of-concept, two SEMs were analyze dynamical properties...

We have utilized an approach that integrates molecular dynamics (MD) simulations with particle swarm optimization (PSO) to accelerate the development of coarse-grained (CG) models hydrocarbons. Specifically, we developed new transferable CG beads, which can be used model hydrocarbons (C5 C17) and reproduce their experimental properties good accuracy. First, PSO method was develop beads decane represented a 2:1 (2-2-2-2-2) mapping scheme. This followed by nonane described hybrid 2-2-3-2 3:1...

Functional groups present in thermo-responsive polymers are known to play an important role aqueous solutions by manifesting their coil-to-globule conformational transition a specific temperature range. Understanding the of these functional and interactions with water is great interest as it may allow us control both nature this transition. In work, polyacrylamide (PAAm), poly(N-isopropylacrylamide) (PNIPAm), poly(N-isopropylmethacrylamide) (PNIPMAm) solvated studied goal discovering...

The adsorption of nonionic surfactants onto hydrophilic nanoparticles (NPs) is anticipated to increase their stability in aqueous medium. While show salinity- and temperature-dependent bulk phase behavior water, the effects these two solvent parameters on surfactant self-assembly NPs are poorly understood. In this study, we combine isotherms, dispersion transmittance, small-angle neutron scattering (SANS) investigate salinity temperature pentaethylene glycol monododecyl ether (C12E5) silica...

Patchy particles occupy an increasingly important space in soft matter research due to their ability assemble into intricate phases and states. Being able fine-tune the interactions among these is essential understanding principles governing self-assembly processes. However, current fabrication techniques often yield patches that deviate chemically physically from native particles, impeding identification of driving forces behind self-assembly. To overcome this challenge, we propose a new...

Understanding the effect of solvent on polymer conformations is a fundamental problem in materials science and engineering. Here, we have developed, first its kind, coarse-grained (CG) model poly(acrylic acid) (PAA) that can reproduce experimental glass transition temperature (Tg) conformation single chain presence explicit solvents along with capturing structure at PAA–solvent interface. The PAA was based CG propionic acid, an analogue monomer. accuracy both acid models validated by...

We have developed transferable coarse-grained (CG) models of the twenty standard amino acids, which can be used to perform molecular dynamics (MD) simulations peptide amphiphiles (PAs) in presence explicit solvent.

Salt-triggered conversion of nanoribbons into nanohelices was studied experimentally and computationally, revealing unexpectedly high ionic conductivity in these self-assembled nanomaterials.

Interactions between water and hydrocarbons play a significant role in chemical, physical, biological processes. Here, we present set of force-field (FF) parameters that define the interactions coarse-grained (CG) hydrocarbon models (An, Y. J. Phys. Chem. B, 2018, 122, 7143−7153) one-site model (Bejagam, K. 1958−1971) developed our recent work. The nonbonded FF various beads are represented by 12-6 Lennard-Jones potential. were optimized to reproduce experimentally measured Gibbs hydration...

The role of charge-asymmetric polyampholytes is unveiled in the liquid–liquid phase separation their mixtures with charge-symmetric polyampholytes.

ABSTRACT In this study, a hybrid microsphere structure with polyhexamethyleneguanidine hydrochloride (PHMG) core and nano‐zinc oxide (Nano‐ZnO) antibacterial additive shell was designed through the reaction extrusion in polypropylene (PP). The realization of enabled successful resolution agglomeration problem Nano‐ZnO achieved synergistic effect between PHMG. Special attention paid to interaction PHMG organic–inorganic hybridization. addition, nonwoven materials different contents were...

Phase-separated biomolecular condensates exhibit a wide range of dynamical properties, which depend on the sequences constituent proteins and RNAs. However, it is unclear to what extent condensate dynamics can be tuned without also changing thermodynamic properties that govern phase separation. Using coarse-grained simulations intrinsically disordered proteins, we show thermodynamics homopolymer are strongly correlated, with increased stability being coincident low mobilities high...

Phase-separated biomolecular condensates exhibit a wide range of dynamical properties, which depend on the sequences constituent proteins and RNAs. However, it is unclear to what extent condensate dynamics can be tuned without also changing thermodynamic properties that govern phase separation. Using coarse-grained simulations intrinsically disordered proteins, we show thermodynamics homopolymer are strongly correlated, with increased stability being coincident low mobilities high...