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1. Predicting mixing free energy using mutual ghosting

   https://doi.org/10.1039/D2ME00109H  

   Shetty, Shreya; Agarwala, Puja; Gomez, Enrique D.; Milner, Scott T. (October 2022, Molecular Systems Design & Engineering)

   The excess free energy of mixing Δ G ex governs the phase behavior of mixtures and controls material properties. It is challenging, however, to measure Δ G ex in simulations. Previously, we developed a method that combines molecular dynamics (MD) simulations with thermodynamic integration along the path of transformation of chains to predict the Flory Huggins interaction parameter χ for polymer mixtures and block copolymers. However, this method is best applied when the constituent molecules of the blends are structurally related. To overcome this limitation, we have developed a new method to predict Δ G ex for mixtures. We perform simulations to induce phase separation within a mixture by gradually weakening the interaction between different species. To compute Δ G ex we measure the thermodynamic work required to modify the interactions and the interfacial energy between the separated phases. We validate our method by applying it first to equimolar mixtures of labeled and unlabeled Lennard-Jones (LJ) beads, and labeled and unlabeled benzene, which results in good agreement with ideal solution theory. Then we compute the excess free energy of mixing for equimolar mixtures of benzene and pyridine, using both united-atom (UA) and all-atom (AA) potentials. Our results using UA potentials predict a value for Δ G ex about four times the experimental value, whereas using AA potentials gives results consistent with experiment, highlighting the need for good potentials to faithfully represent mixture behavior. 

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2. Refining amino acid hydrophobicity for dynamics simulation of membrane proteins

   https://doi.org/10.7717/peerj.4230  

   Hills, Jr (January 2018, PeerJ)

   Coarse-grained (CG) models have been successful in simulating the chemical properties of lipid bilayers, but accurate treatment of membrane proteins and lipid-protein molecular interactions remains a challenge. The CgProt force field, original developed with the multiscale coarse graining method, is assessed by comparing the potentials of mean force for sidechain insertion in a DOPC bilayer to results reported for atomistic molecular dynamics simulations. Reassignment of select CG sidechain sites from the apolar to polar site type was found to improve the attractive interfacial behavior of tyrosine, phenylalanine and asparagine as well as charged lysine and arginine residues. The solvation energy at membrane depths of 0, 1.3 and 1.7 nm correlates with experimental partition coefficients in aqueous mixtures of cyclohexane, octanol and POPC, respectively, for sidechain analogs and Wimley-White peptides. These experimental values serve as important anchor points in choosing between alternate CG models based on their observed permeation profiles, particularly for Arg, Lys and Gln residues where the all-atom OPLS solvation energy does not agree well with experiment. Available partitioning data was also used to reparameterize the representation of the peptide backbone, which needed to be made less attractive for the bilayer hydrophobic core region. The newly developed force field, CgProt 2.4, correctly predicts the global energy minimum in the potentials of mean force for insertion of the uncharged membrane-associated peptides LS3 and WALP23. CgProt will find application in studies of lipid-protein interactions and the conformational properties of diverse membrane protein systems. 

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3. Compactness estimates for minimizers of the Alt-Phillips functional of negative exponents

   https://doi.org/10.1515/ans-2022-0055  

   De Silva, Daniela; Savin, Ovidiu (January 2023, Advanced Nonlinear Studies)

   Abstract We investigate the rigidity of global minimizers u ≥ 0 u\ge 0 of the Alt-Phillips functional involving negative power potentials ∫ Ω ( ∣ ∇ u ∣ 2 + u − γ χ { u > 0 } ) d x , γ ∈ ( 0 , 2 ) , \mathop{\int }\limits_{\Omega }(| \nabla u{| }^{2}+{u}^{-\gamma }{\chi }_{\left\{u\gt 0\right\}}){\rm{d}}x,\hspace{1.0em}\gamma \in \left(0,2), when the exponent γ \gamma is close to the extremes of the admissible values. In particular, we show that global minimizers in R n {{\mathbb{R}}}^{n} are one-dimensional if γ \gamma is close to 2 and n ≤ 7 n\le 7 , or if γ \gamma is close to 0 and n ≤ 4 n\le 4 . 

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4. The ab initio potential energy curves of atom pairs and transport properties of high-temperature vapors of Cu and Si and their mixtures with He, Ar, and Xe gases

   https://doi.org/10.1039/d2cp04981c  

   Kayang, Kevin W.; Volkov, Alexey N.; Zhilyaev, Petr A.; Sharipov, Felix (February 2023, Physical Chemistry Chemical Physics)

   The potential energy curves (PECs) for the homonuclear He–He, Ar–Ar, Cu–Cu, and Si–Si dimers, as well as heteronuclear Cu–He, Cu–Ar, Cu–Xe, Si–He, Si–Ar, and Si–Xe dimers, are obtained in quantum Monte Carlo (QMC) calculations. It is shown that the QMC method provides the PECs with an accuracy comparable with that of the state-of-the-art coupled cluster singles and doubles with perturbative triples corrections [CCSD(T)] calculations. The QMC data are approximated by the Morse long range (MLR) and (12-6) Lennard-Jones (LJ) potentials. The MLR and LJ potentials are used to calculate the deflection angles in binary collisions of corresponding atom pairs and transport coefficients of Cu and Si vapors and their mixtures with He, Ar, and Xe gases in the range of temperature from 100 K to 10 000 K. It is shown that the use of the LJ potentials introduces significant errors in the transport coefficients of high-temperature vapors and gas mixtures. The mixtures with heavy noble gases demonstrate anomalous behavior when the viscosity and thermal conductivity can be larger than that of the corresponding pure substances. In the mixtures with helium, the thermal diffusion factor is found to be unusually large. The calculated viscosity and diffusivity are used to determine parameters of the variable hard sphere and variable soft sphere molecular models as well as parameters of the power-law approximations for the transport coefficients. The results obtained in the present work include all information required for kinetic or continuum simulations of dilute Cu and Si vapors and their mixtures with He, Ar, and Xe gases. 

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5. Assignment-free chirality detection in unknown samples via microwave three-wave mixing

   https://doi.org/10.1038/s42004-022-00641-3  

   Koumarianou, Greta; Wang, Irene; Satterthwaite, Lincoln; Patterson, David (March 2022, Communications Chemistry)

   Abstract Straightforward identification of chiral molecules in multi-component mixtures of unknown composition is extremely challenging. Current spectrometric and chromatographic methods cannot unambiguously identify components while the state of the art spectroscopic methods are limited by the difficult and time-consuming task of spectral assignment. Here, we introduce a highly sensitive generalized version of microwave three-wave mixing that uses broad-spectrum fields to detect chiral molecules in enantiomeric excess without any prior chemical knowledge of the sample. This method does not require spectral assignment as a necessary step to extract information out of a spectrum. We demonstrate our method by recording three-wave mixing spectra of multi-component samples that provide direct evidence of enantiomeric excess. Our method opens up new capabilities in ultrasensitive phase-coherent spectroscopic detection that can be applied for chiral detection in real-life mixtures, raw products of chemical reactions and difficult to assign novel exotic species. 

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