Local Volume Concentration, Packing Domains and Scaling Properties of Chromatin.

We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions that can capture the observed behavior across imaging and sequencing based measures of chromatin organization. From nucleosome to chromosome scales, the model captures the overall chromatin organization as a corrugated system, with dense and dilute regions alternating in a manner that resembles the mixing of two disordered bi-continuous phases. This particular organizational topology is a consequence of the multiplicity of interactions and processes ocurring in the nuclei, and mimicked by the proposed return rules. Single configuration properties and ensemble averages show a robust agreement between theoretical and experimental results including chromatin volume concentration, contact probability, packing domain identification and size characterization, and packing scaling behavior. Model and experimental results suggest that there is an inherent chromatin organization regardless of the cell character and resistent to external forcings such as Rad21 degradation.

Local Volume Concentration, Packing Domains and Scaling Properties of Chromatin.

We propose the Self Returning Excluded Volume (SR-EV) model for the structure of chromatin based on stochastic rules and physical interactions that is able to capture the observed behavior across imaging and sequencing based measures of chromatin organization. The SR-EV model takes the return rules of the Self Returning Random Walk, incorporates excluded volume interactions, chain connectivity and expands the length scales range from 10 nm to over 1 micron. The model is computationally fast and we created thousands of configurations that we grouped in twelve different ensembles according to the two main parameters of the model. The analysis of the configurations was done in a way completely analogous to the experimental treatments used to determine chromatin volume concentration, contact probability, packing domain identification and size characterization, and packing scaling behavior. We find a robust agreement between the theoretical and experimental results. The overall organization of the model chromatin is corrugated, with dense packing domains alternating with a very dilute regions in a manner that resembles the mixing of two disordered bi-continuous phases. The return rules combined with excluded volume interactions lead to the formation of packing domains. We observed a transition from a short scale regime to a long scale regime occurring at genomic separations of ~ 4 × 104 base pairs or ~ 100 nm in distance. The contact probability reflects this transition with a change in the scaling exponent from larger than -1 to approximately -1. The analysis of the pair correlation function reveals that chromatin organizes following a power law scaling with exponent D∈{2,3} in the transition region between the short and long distance regimes.

Analysis of three-dimensional chromatin packing domains by chromatin scanning transmission electron microscopy (ChromSTEM).

Chromatin organization over multiple length scales plays a critical role in the regulation of transcription. Deciphering the interplay of these processes requires high-resolution, three-dimensional, quantitative imaging of chromatin structure in vitro. Herein, we introduce ChromSTEM, a method that utilizes high-angle annular dark-field imaging and tomography in scanning transmission electron microscopy combined with DNA-specific staining for electron microscopy. We utilized ChromSTEM for an in-depth quantification of 3D chromatin conformation with high spatial resolution and contrast, allowing for characterization of higher-order chromatin structure almost down to the level of the DNA base pair. Employing mass scaling analysis on ChromSTEM mass density tomograms, we observed that chromatin forms spatially well-defined higher-order domains, around 80 nm in radius. Within domains, chromatin exhibits a polymeric fractal-like behavior and a radially decreasing mass-density from the center to the periphery. Unlike other nanoimaging and analysis techniques, we demonstrate that our unique combination of this high-resolution imaging technique with polymer physics-based analysis enables us to (i) investigate the chromatin conformation within packing domains and (ii) quantify statistical descriptors of chromatin structure that are relevant to transcription. We observe that packing domains have heterogeneous morphological properties even within the same cell line, underlying the potential role of statistical chromatin packing in regulating gene expression within eukaryotic nuclei.

First-Principles Molecular Dynamics in Metal-Halide Perovskites: Contrasting Generalized Gradient Approximation and Hybrid Functionals.

First-principles molecular dynamics (FPMD) represents a valuable tool to probe dynamical properties of metal-halide perovskites (MHPs) which are key to their success in optoelectronic devices. Most FPMD studies rely on generalized gradient approximation (GGA) functionals for computational efficiency matters, while hybrid functionals, although computationally demanding, are usually needed to accurately describe structural and electronic properties of MHPs. This Letter reports FPMD simulations on CsPbI3 based on the hybrid PBE0 functional. Our results demonstrate that PBE0 leads to lattice parameters and phonon modes in excellent agreement with experimental data, while GGA results overestimate the lattice parameter and the electronic band gap and underestimate the phonon energies. Our FPMD results also shed light on anharmonic effects and double-well instabilities in the octahedral tilting, highlighting a lowered free energy barrier for PBE0 and farther separated potential wells. Our results suggest that hybrid functionals are required to accurately describe crystal structure, lattice dynamics, and anharmonicity in MHPs.

Ultrafast Transfer and Transient Entrapment of Photoexcited Mg Electron in Mg@C_{60}.

Electron relaxation is studied in endofullerene Mg@C_{60} after an initial localized photoexcitation in Mg by nonadiabatic molecular dynamics simulations. Two approaches to the electronic structure of the excited electronic states are used: (i) an independent particle approximation based on a density-functional theory description of molecular orbitals and (ii) a configuration-interaction description of the many-body effects. Both methods exhibit similar relaxation times, leading to an ultrafast decay and charge transfer from Mg to C_{60} within tens of femtoseconds. Method (i) further elicits a transient trap of the transferred electron that can delay the electron-hole recombination. Results shall motivate experiments to probe these ultrafast processes by two-photon transient absorption or photoelectron spectroscopy in gas phase, in solution, or as thin films.

Adsorption and isomerization of glyoxal and methylglyoxal at the air/hydroxylated silica surface.

We present results from molecular dynamics simulations coupled with enhanced sampling techniques on the adsorption and isomerization of glyoxal (GL) and methylglyoxal (MG) at the air/hydroxylated silica (α-Quartz) interface. GL and MG are two organic compounds present in the atmosphere as oxidation products of both biogenic and anthropogenic precursors. By adsorption and hydration on liquid droplets or wetted dust particles, they can enable aerosol growth in the atmosphere. Moreover, thanks to the different polar characters of their trans and cis conformers, GL and MG have been suggested as possible molecular switches capable of responding to changes in solvent polarity. Here, we show that the hydroxylated silica surface does not significantly catalyze the trans-to-cis isomerization, but it stabilizes the cis-isomers, indicating a higher interfacial cis/trans relative concentration compared to the gas phase. Moreover, adsorbed GL prefers to lie parallel on the silica surface, while adsorbed MG shows a tilted orientation. In particular, we report the aldehyde group pointing upward (downward) to the gas phase (to the silica surface) in trans-MG (cis-MG). These results will help in the rationalization of upcoming experimental and modeling work on the adsorption of ketonic compounds on dust aerosols, while it clarifies the catalytic role of the solid substrate surface in promoting conformational changes.

Self-assembly of Pseudo-Dipolar Nanoparticles at Low Densities and Strong Coupling.

Nanocolloids having directional interactions are highly relevant for designing new self-assembled materials easy to control. In this article we report stochastic dynamics simulations of finite-size pseudo-dipolar colloids immersed in an implicit dielectric solvent using a realistic continuous description of the quasi-hard Coulombic interaction. We investigate structural and dynamical properties near the low-temperature and highly-diluted limits. This system self-assembles in a rich variety of string-like configurations, depicting three clearly distinguishable regimes with decreasing temperature: fluid, composed by isolated colloids; string-fluid, a gas of short string-like clusters; and string-gel, a percolated network. By structural characterization using radial distribution functions and cluster properties, we calculate the state diagram, verifying the presence of string-fluid regime. Regarding the string-gel regime, we show that the antiparallel alignment of the network chains arises as a novel self-assembly mechanism when the characteristic interaction energy exceeds the thermal energy in two orders of magnitude, ud/kBT ≈ 100. This is associated to relevant structural modifications in the network connectivity and porosity. Furthermore, our results give insights about the dynamically-arrested nature of the string-gel regime, where we show that the slow relaxation takes place in minuscule energy steps that reflect local rearrangements of the network.

Crystallization properties of arsenic doped GST alloys.

We present the enhanced properties observed in the phase change memory alloy Ge2Sb2Te5 (GST) when doped with arsenic. Although arsenic is known as a toxic element, our observations show that significant improvement can be obtained in GST systems on thermal stability, transition temperature between amorphous and crystalline phases and switching behaviors when doping with arsenic. Though both the GST and arsenic doped GST are amorphous in the as-deposited state, only GST alloy turns to crystalline NaCl-type structure after annealing at 150 °C for 1 h. Results from the resistance versus temperature study show a systematic increase in the transition temperature and resistivity in the amorphous and crystalline states when the arsenic percentage in the GST alloy increases. The crystallization temperature (Tc) of (GST)0.85As0.15 is higher than the Tc observed in GST. Optical band gap (Eopt) values of the as-deposited films show a clear increasing trend; 0.6 eV for GST to 0.76 eV for (GST)0.85As0.15. The decreases in Eopt for the samples annealed at higher temperatures shows significant optical contrast between the as-deposited and annealed samples. Though all (GST)1-xAsx alloys show memory switching behaviors, threshold switching voltages (VT) of the studied alloys show an increasing trend with arsenic doping. For (GST)0.85As0.15, VT is about 5.2 V, which is higher than GST (4.0 V). Higher transition temperature and higher threshold switching values show arsenic doping in GST can enhance the memory device properties by improving the thermal stability and data readability. Understanding the doping effect on the GST is important to understand its crystallization properties. Structure properties of amorphous GST, Ge2Sb2-0.3As0.3Te5 and (GST)0.85As0.15 models were studied using first principles molecular dynamics simulations, compared their partial radial distribution functions, and q parameter order. Arsenic doping into GST features interesting structural and electronic effects revealed by the radial distribution functions, q order parameter and band gap value, in line with the experimental findings.

Tuning the Stereoselectivity and Solvation Selectivity at Interfacial and Bulk Environments by Changing Solvent Polarity: Isomerization of Glyoxal in Different Solvent Environments.

Conformational isomerism plays a central role in organic synthesis and biological processes; however, effective control of isomerization processes still remains challenging and elusive. Here, we propose a novel paradigm for conformational control of isomerization in the condensed phase, in which the polarity of the solvent determines the relative concentration of conformers at the interfacial and bulk regions. By the use of state-of-the-art molecular dynamics simulations of glyoxal in different solvents, we demonstrate that the isomerization process is dipole driven: the solvent favors conformational changes toward conformers having molecular dipoles that better match its polar character. Thus, the solvent polarity modulates the conformational change, stabilizing and selectively segregating in the bulk vs the interface one conformer with respect to the others. The findings in this paper have broader implications affecting systems involving compounds with conformers of different polarity. This work suggests novel mechanisms for tuning the catalytic activity of surfaces in conformationally controlled (photo)chemical reactions and for designing a new class of molecular switches that are active in different solvent environments.

A surface-stabilized ozonide triggers bromide oxidation at the aqueous solution-vapour interface.

Oxidation of bromide in aqueous environments initiates the formation of molecular halogen compounds, which is important for the global tropospheric ozone budget. In the aqueous bulk, oxidation of bromide by ozone involves a [Br•OOO-] complex as intermediate. Here we report liquid jet X-ray photoelectron spectroscopy measurements that provide direct experimental evidence for the ozonide and establish its propensity for the solution-vapour interface. Theoretical calculations support these findings, showing that water stabilizes the ozonide and lowers the energy of the transition state at neutral pH. Kinetic experiments confirm the dominance of the heterogeneous oxidation route established by this precursor at low, atmospherically relevant ozone concentrations. Taken together, our results provide a strong case of different reaction kinetics and mechanisms of reactions occurring at the aqueous phase-vapour interface compared with the bulk aqueous phase.Heterogeneous oxidation of bromide in atmospheric aqueous environments has long been suspected to be accelerated at the interface between aqueous solution and air. Here, the authors provide spectroscopic, kinetic and theoretical evidence for a rate limiting, surface active ozonide formed at the interface.

Mapping the Free Energy of Lithium Solvation in the Protic Ionic Liquid Ethylammonuim Nitrate: A Metadynamics Study.

Understanding lithium solvation and transport in ionic liquids is important due to their possible application in electrochemical devices. Using first-principles simulations aided by a metadynamics approach we study the free-energy landscape for lithium ions at infinite dilution in ethylammonium nitrate, a protic ionic liquid. We analyze the local structure of the liquid around the lithium cation and obtain a quantitative picture in agreement with experimental findings. Our simulations show that the lowest two free energy minima correspond to conformations with the lithium ion being solvated either by three or four nitrate ions with a transition barrier between them of 0.2 eV. Other less probable conformations having different solvation pattern are also investigated.

Effect of Shear History on Rheology of Time-Dependent Colloidal Silica Gels.

This paper presents a rheological study describing the effects of shear on the flow curves of colloidal gels prepared with different concentrations of fumed silica (4%, 5%, 6%, and 7%) and a hydrophobic solvent (Hydrocarbon fuel, JP-8). Viscosity measurements as a function of time were carried out at different shear rates (10, 50, 100, 500, and 1000 s-1), and based on this data, a new structural kinetics model was used to describe the system. Previous work has based the analysis of time dependent fluids on the viscosity of the intact material, i.e., before it is sheared, which is a condition very difficult to achieve when weak gels are tested. The simple action of loading the gel in the rheometer affects its structure and rheology, and the reproducibility of the measurements is thus seriously compromised. Changes in viscosity and viscoelastic properties of the sheared material are indicative of microstructural changes in the gel that need to be accounted for. Therefore, a more realistic method is presented in this work. In addition, microscopical images (Cryo-SEM) were obtained to show how the structure of the gel is affected upon application of shear.

Hydrogen bonding and orientation effects on the accommodation of methylamine at the air-water interface.

Methylamine is an abundant amine compound detected in the atmosphere which can affect the nature of atmospheric aerosol surfaces, changing their chemical and optical properties. Molecular dynamics simulation results show that methylamine accommodation on water is close to unity with the hydrophilic head group solvated in the interfacial environment and the methyl group pointing into the air phase. A detailed analysis of the hydrogen bond network indicates stronger hydrogen bonds between water and the primary amine group at the interface, suggesting that atmospheric trace gases will likely react with the methyl group instead of the solvated amine site. These findings suggest new chemical pathways for methylamine acting on atmospheric aerosols in which the methyl group is the site of orientation specific chemistry involving its conversion into a carbonyl site providing hydrophilic groups for uptake of additional water. This conversion may explain the tendency of aged organic aerosols to form cloud condensation nuclei. At the same time, formation of NH2 radical and formaldehyde is suggested to be a new source for NH2 radicals at aerosol surfaces, other than by reaction of absorbed NH3. The results have general implications for the chemistry of other amphiphilic organics, amines in particular, at the surface of atmospherically relevant aerosols.

Dynamic Heterogeneity in the Monoclinic Phase of CCl4.

Carbon tetrachloride (CCl4) is one of the simplest compounds having a translationally stable monoclinic phase while exhibiting a rich rotational dynamics below 226 K. Recent nuclear quadrupolar resonance experiments revealed that the dynamics of CCl4 is similar to that of the other members of the isostructural series CBrnCl4-n, suggesting that the universal relaxation features of canonical glasses such as α and ß relaxation are also present in nonglass formers. Using molecular dynamics simulations we studied the rotational dynamics in the monoclinic phase of CCl4. The molecules undergo C3-type jump-like rotations around each one of the four C-Cl bonds. The rotational dynamics is very well described with a master equation using as the only input the rotational rates measured from the simulated trajectories. It is found that the heterogeneous dynamics emerges from faster and slower modes associated with different rotational axes, which have fixed orientations relative to the crystal and are distributed among the four nonequivalent molecules of the unit cell.

Self-assembled nanoparticle of common food constituents that carries a sparingly soluble small molecule.

A previously reported nanoparticle formed through the self-assembly of common food constituents (amylose, protein, and fatty acids) was shown to have the capacity to carry a sparingly soluble small molecule (1-naphthol) in a dispersed system. Potentiometric titration showed that 1-naphthol locates in the lumen of the amylose helix of the nanoparticle. This finding was further supported by calorimetric measurements, showing higher enthalpies of dissociation and reassociation in the presence of 1-naphthol. Visually, the 1-naphthol-loaded nanoparticle appeared to be well-dispersed in aqueous solution. Molecular dynamics simulation showed that the self-assembly was favorable, and at 500 ns, the 1-naphthol molecule resided in the helix of the amylose lumen in proximity to the hydrophobic tail of the fatty acid. Thus, sparingly soluble small molecules, such as some nutraceuticals or drugs, could be incorporated and delivered by this soft nanoparticle carrier.

Ab initio study of the reaction of ozone with bromide ion.

Surface level ozone destruction in polar environments may be initiated by oxidation of bromide ions by ozone, ultimately leading to Br2 production. Ab initio calculations are used to support the development of atmospheric chemistry models, but errors can occur in study of the bromide-ozone reaction due to inappropriate treatment of the many-electron species and the ionic nature of the reaction. In this work, a high level ab initio study is used to take into account the electronic correlation and the polarization effects. Our results show three possible pathways for the reaction. In particular, we find that this process, though endothermic on the singlet spin state surface, can be energetically feasible on the triplet surface. The triplet surface can be reached through photoexcitation of ozone or by the spin crossing of the potential energy surface. Because this process is known to occur in the dark, it may be that it occurs after intersystem crossing to a triplet surface. This paper also provides a starting point calibration for any future ab initio calculation studies of the bromide-ozone reaction, from the gas to the condensed phase.

Structure and dynamics of [PF6][P(1,2,2,4)] from molecular dynamics simulations.

Diethyl(methyl)(isobutyl)phosphonium hexafluorophosphate, [PF6][P(1,2,2,4)], is an organic ionic plastic crystal with potential uses as a solid electrolyte in storage and light harvesting devices. In this work, we present a molecular dynamics simulation study for this material covering an extended temperature range, from 175 to 500 K. The simulations predict a transition from the crystalline to a semi plastic phase at 197 K, the onset of cation jump-like rotations at 280 K, a third transition at 340 K to a full plastic phase, and melting to 450 K. Overall, the simulations show a good agreement with the experimental findings, providing a wealth of detail in the structural and dynamic properties of the system.

Cooperative dynamic and diffusion behavior above and below the dynamical crossover of supercooled water.

Using extensive molecular dynamics simulations combined with a novel approach to analyze the molecular displacements we analyzed the change in the dynamics above and below the crossover temperature T(x) for supercooled water. Our findings suggest that the crossover from fragile to strong glass former occurring at T(x) is related with a change in the diffusion mechanism evidencing the presence of jump-like diffusion at lower temperatures. Also we observe that fluctuations of the local environments are intimately connected with fluctuations in the size and the amount of cooperative cluster of mobile molecules, and in particular we find a highly cooperative nature of the motion at low temperatures.

The water supercooled regime as described by four common water models.

The temperature scale of simple water models in general does not coincide with the natural one. Therefore, in order to make a meaningful evaluation of different water models, a temperature rescaling is necessary. In this paper, we introduce a rescaling using the melting temperature and the temperature corresponding to the maximum of the heat capacity to evaluate four common water models (TIP4P-Ew, TIP4P-2005, TIP5P-Ew and Six-Sites) in the supercooled regime. Although all the models show the same general qualitative behavior, the TIP5P-Ew appears as the best representation of the supercooled regime when the rescaled temperature is used. We also analyze, using thermodynamic arguments, the critical nucleus size for ice growth. Finally, we speculate on the possible reasons why atomistic models do not usually crystalize while the coarse grained mW model do crystallize.