Shikha Nangia

Effects of nanoparticle charge and shape anisotropy on translocation through cell membranes

Nanotoxicity is becoming a major concern as the use of nanoparticles in imaging, therapeutics, diagnostics, catalysis, sensing, and energy harvesting continues to grow dramatically. The tunable functionalities of the nanoparticles offer unique chemical interactions in the translocation process through cell membranes. The overall translocation rate of the nanoparticle can vary immensely on the basis of the charge of the surface functionalization along with shape and size. Using advanced molecular dynamics simulation techniques, we compute translocation rate constants of functionalized cone-, cube-, rod-, rice-, pyramid-, and sphere-shaped nanoparticles through lipid membranes. The computed results indicate that depending on the nanoparticle shape and surface functionalization charge, the translocation rates can span 60 orders of magnitude. Unlike isotropic nanoparticles, positively charged, faceted, rice-shaped nanoparticles undergo electrostatics-driven reorientation in the vicinity of the membrane to maximize their contact area and translocate instantaneously, disrupting lipid self-assembly and thereby causing significant membrane damage. In contrast, negatively charged nanoparticles are electrostatically repelled from the cell membrane and are less likely to translocate. Differences in translocation rates among various shapes may have implications on the structural evolution of pathogens from spherical to rodlike morphologies for enhanced efficacy.

Reaction Rates and Dissolution Mechanisms of Quartz as a Function of pH

In this computational study, we present the dissolution rates for quartz as a function of pH at 298 K. At any given pH, the dissolution of the quartz surface depends on the distribution of protonated, deprotonated, or neutral species. The dissolution mechanism for each of these three species was investigated by ab initio electronic structure calculations to obtain the reaction profile. Using the barrier height along with the partition functions for the transition state and the reactants in the rate-limiting steps, we calculated the TST rate constants for the reactions for the temperature range of 200-500 K. At 298 K the rate constant (s-1) for the dissolution of neutral species was found to be several orders of magnitude smaller than the rate-limiting steps for the protonated and deprotonated species. The values of the rate constants were used in the rate law expression to calculate the overall dissolution rate (mol m-2 s-1) at a given pH. The calculated rates were compared to previously reported experimental and theoretical rates and were found to be in good agreement over 2-12 pH range.

Direct calculation of coupled diabatic potential-energy surfaces for ammonia and mapping of a four-dimensional conical intersection seam.

We used multiconfiguration quasidegenerate perturbation theory and the fourfold-way direct diabatization scheme to calculate ab initio potential-energy surfaces at 3600 nuclear geometries of NH3. The calculations yield the adiabatic and diabatic potential-energy surfaces for the ground and first electronically excited singlet states and also the diabatic coupling surfaces. The diabatic surfaces and coupling were fitted analytically to functional forms to obtain a permutationally invariant 2 x 2 diabatic potential-energy matrix. An analytic representation of the adiabatic potential-energy surfaces is then obtained by diagonalizing the diabatic potential-energy matrix. The analytic representation of the surfaces gives an analytic representation of the four-dimensional conical intersection seam which is discussed in detail.

Army ants algorithm for rare event sampling of delocalized nonadiabatic transitions by trajectory surface hopping and the estimation of sampling errors by the bootstrap method

The most widely used algorithm for Monte Carlo sampling of electronic transitions in trajectory surface hopping (TSH) calculations is the so-called anteater algorithm, which is inefficient for sampling low-probability nonadiabatic events. We present a new sampling scheme (called the army ants algorithm) for carrying out TSH calculations that is applicable to systems with any strength of coupling. The army ants algorithm is a form of rare event sampling whose efficiency is controlled by an input parameter. By choosing a suitable value of the input parameter the army ants algorithm can be reduced to the anteater algorithm (which is efficient for strongly coupled cases), and by optimizing the parameter the army ants algorithm may be efficiently applied to systems with low-probability events. To demonstrate the efficiency of the army ants algorithm, we performed atom-diatom scattering calculations on a model system involving weakly coupled electronic states. Fully converged quantum mechanical calculations were performed, and the probabilities for nonadiabatic reaction and nonreactive deexcitation (quenching) were found to be on the order of 10(-8). For such low-probability events the anteater sampling scheme requires a large number of trajectories ( approximately 10(10)) to obtain good statistics and converged semiclassical results. In contrast by using the new army ants algorithm converged results were obtained by running 10(5) trajectories. Furthermore, the results were found to be in excellent agreement with the quantum mechanical results. Sampling errors were estimated using the bootstrap method, which is validated for use with the army ants algorithm.

Ab Initio Investigation of Dissolution Mechanisms in Aluminosilicate Minerals

The reactions of aluminosilicate clusters with water are investigated using ab initio calculations. There are several reaction sites on a mineral surface, and, in the case of aluminosilicates, the dissolution chemistry is dictated by chemically distinct surface termination sites: Al and Si. Environmental factors such as pH determine the protonation state and configuration around these terminal sites. The dissolution mechanisms for Al- and Si-terminated sites in protonated, neutral, and deprotonated states are determined using density functional theory calculations. In all protonation states, Si are tetra-coordinated; however, the ability of Al to exist in tetra-, penta-, and hexa-coordination states makes the dissolution mechanisms for the two types of terminal sites fundamentally different. The calculated barrier heights for Al-terminated sites are predicted to be lower than those for Si-terminated sites, a trend that has been observed in experimental studies. The sensitivity of the calculations on the choice of density functionals and basis sets is tested using three functionals: B3LYP, PBE1PBE, and M05-2X, in combination with the 6-311+G(d,p) and MG3S basis sets. For all these calculations, the geometries of the stationary points along the reaction path and the barrier heights are presented.

Simulating Gram-Negative Bacterial Outer Membrane: A Coarse Grain Model.

The cell envelope of Gram-negative bacteria contains a lipopolysaccharide (LPS) rich outer membrane that acts as the first line of defense for bacterial cells in adverse physical and chemical environments. The LPS macromolecule has a negatively charged oligosaccharide domain that acts as an ionic brush, limiting the permeability of charged chemical agents through the membrane. Besides the LPS, the outer membrane has radially extending O-antigen polysaccharide chains and β-barrel membrane proteins that make the bacterial membrane physiologically unique compared to phospholipid cell membranes. Elucidating the interplay of these contributing macromolecular components and their role in the integrity of the bacterial outer membrane remains a challenge. To bridge the gap in our current understanding of the Gram-negative bacterial membrane, we have developed a coarse grained force field for outer membrane that is computationally affordable for simulating dynamical process over physiologically relevant time scales. The force field was benchmarked against available experimental and atomistic simulations data for properties such as membrane thickness, density profiles of the residues, area per lipid, gel to liquid-crystalline phase transition temperatures, and order parameters. More than 17 membrane compositions were studied with a combined simulation time of over 100 μs. A comparison of simulated structural and dynamical properties with corresponding experimental data shows that the developed force field reproduces the overall physiology of LPS rich membranes. The affordability of the developed model for long time scale simulations can be instrumental in determining the mechanistic aspects of the antimicrobial action of chemical agents as well as assist in designing antimicrobial peptides with enhanced outer membrane permeation properties.

Ab initio study of dissolution and precipitation reactions from the edge, kink, and terrace sites of quartz as a function of pH

In this study, the fundamental concept of mineral surface roughness and the role it plays on the dissolution and precipitation processes using ab initio density functional theory calculations, have been investigated. To understand the topological contribution to the dissolution and precipitation rates of quartz, a systematic study was designed to determine the reaction mechanisms and barrier heights of the forward reaction of hydrolysis of–Si(OH)3 group from underlying edge, kink, and terrace sites. The edge and kink sites are topological features on mineral surfaces that are bound to the bulk with fewer Si–O–Si bridge bonds than a terrace site, a factor that can be significant in the dissolution process. In this work, the local arrangement of atoms on the underlying sites is included by systematically increasing the Si–O–Si bridging to represent the edge, kink, and terrace sites under ambient conditions in the neutral, deprotonated, and protonated states. Nine reaction profiles were studied using the M05-2X density functional with 6–31 + G(d,p) basis set. The results show that hydrolysis of the–Si(OH)3 group and the back reactions are not too sensitive to the underlying edge, kink, and terrace site. The barrier height data also explain the experimentally observed dissolution rate over the entire pH range, especially the tremendously high dissolution rate below pH 2.

Multiscale Approach to Investigate Self-Assembly of Telodendrimer Based Nanocarriers for Anticancer Drug Delivery

Delivery of poorly soluble anticancer drugs can be achieved by employing polymeric drug delivery systems, capable of forming stable self-assembled nanocarriers with drug encapsulated within their hydrophobic cores. Computational investigations can aid the design of efficient drug-delivery platforms; however, simulations of nanocarrier self-assembly process are challenging due to high computational cost associated with the large system sizes (millions of atoms) and long time scales required for equilibration. In this work, we overcome this challenge by employing a multiscale computational approach in conjunction with experiments to analyze the role of the individual building blocks in the self-assembly of a highly tunable linear poly(ethylene glycol)-b-dendritic oligo(cholic acid) block copolymer called telodendrimer. The multiscale approach involved developing a coarse grained description of the telodendrimer, performing simulations over several microseconds to capture the self-assembly process, followed by reverse mapping of the coarse grained system to atomistic representation for structural analysis. Overcoming the computational bottleneck allowed us to run multiple self-assembly simulations and determine average size, drug-telodendrimer micellar stoichiometry, optimal drug loading capacity, and atomistic details such hydrogen-bonding and solvent accessible area of the nanocarrier. Computed results are in agreement with the experimental data, highlighting the success of the multiscale approach applied here.

Advanced Monte Carlo approach to study evolution of quartz surface during the dissolution process.

A newly developed Monte Carlo (MC) algorithm designed to study the complex interplay of dissolution and precipitation reactions on mineral surface is presented. This algorithm utilizes existing advanced reactive and configurational-biased MC techniques with new protocols specific for mineral-water interfaces. This time-independent methodology is especially advantageous for studying the kinetically slow quartz-water dissolution process. The aim is to use this method to understand the role of the local arrangement of reactive sites and surface topography in the surface evolution during dissolution. The simulations were performed in neutral pH medium, and two possible dissolution mechanisms were tested. The results indicate that out of the direct and stepwise mechanisms, the direct mechanism leads to complete dissolution that is not experimentally observed in the natural environment. On the other hand, the stepwise dissolution is more realistic, as it resembles the experimentally observed steady-state dissolution of the quartz-water system. These simulations identify the least coordinated surface sites (Q(1)) as the primary reactive site for hydrolysis and precipitation. Other surface sites (Q(2) and Q(3)) also undergo hydrolysis, but they are sterically hindered and are turned passive by precipitating Q(1) groups. The conclusions from the simulations are dominated by the surface topology of quartz; thus, we believe that the results are applicable for other polymorphs of silica and other protonation conditions.

Molecular Architecture of the Blood Brain Barrier Tight Junction Proteins--A Synergistic Computational and In Vitro Approach.

The blood-brain barrier (BBB) constituted by claudin-5 tight junctions is critical in maintaining the homeostasis of the central nervous system, but this highly selective molecular interface is an impediment for therapeutic interventions in neurodegenerative and neurological diseases. Therapeutic strategies that can exploit the paracellular transport remain elusive due to lack of molecular insights of the tight junction assembly. This study focuses on analyzing the membrane driven cis interactions of claudin-5 proteins in the formation of the BBB tight junctions. We have adopted a synergistic approach employing in silico multiscale dynamics and in vitro cross-linking experiments to study the claudin-5 interactions. Long time scale simulations of claudin-5 monomers, in seven different lipid compositions, show formation of cis dimers that subsequently aggregate into strands. In vitro formaldehyde cross-linking studies also conclusively show that cis-interacting claudin-5 dimers cross-link with short methylene spacers. Using this synergistic approach, we have identified five unique dimer interfaces in our simulations that correlate with the cross-linking experiments, four of which are mediated by transmembrane (TM) helices and the other mediated by extracellular loops (ECL). Potential of mean force calculations of these five dimers revealed that the TM mediated interfaces, which can have distinctive leucine zipper interactions in some cases, are more stable than the ECL mediated interface. Additionally, simulations show that claudin-5 dimerization is significantly influenced by the lipid microenvironment. This study captures the fundamental interactions responsible for the BBB tight junction assembly and offers a framework for extending this work to other tight junctions found in the body.