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Developing fouling-resistant materials is of paramount interest in marine industries and biomedical applications. In this work, we studied the interfacial hydration and surface-protein interactions of the amphiphilic brush surface functionalized with hybrid hydrophilic trimethylamine N -oxide (TMAO) and hydrophobic pentafluoroethyl groups using a combination of atomistic molecular dynamics simulations and free-energy computations. Our results show that while the interfacial hydration density of the amphiphilic surface slightly decreases with the introduction of small fluorocarbons compared to that of the pure TMAO-functionalized surface, the amphiphilic surface remains relatively strong in resisting protein adsorption. The nanosized clustering of hydrophobic fluorine atoms on the top of the amphiphilic brush surface introduces weak protein adsorption; however, due to the strong interfacial hydration and weak hydrophobic interaction, the amphiphilic surface exhibits sufficient antibiofouling activities. Our fundamental studies will be critical for the discovery of marine fouling-resistant coating surfaces.

Biological nanopores are increasingly used in molecular sensing due to their single-molecule sensitivity. The detection of per- and polyfluoroalkyl substances (PFAS) like perfluorooctanoic acid and perfluorooctane sulfonic acid is critical due to their environmental prevalence and toxicity. Here, we investigate selective interactions between PFAS and four cyclodextrin (CD) variants (α-, β-, γ-, and 2-hydroxypropyl-γ-CD) within an α-hemolysin nanopore. We demonstrate that PFAS molecules can be electrochemically sensed by interacting with a γ-CD in a nanopore. Using HP-γ-CDs with increased steric resistance, we can identify homologs of the perfluoroalkyl carboxylic acid and the perfluoroalkyl sulfonic acid families and detect common PFAS in drinking water at 0.4 to 2 parts per million levels, which are further lowered to 400 parts per trillion by sample preconcentration. Molecular dynamics simulations reveal the underlying chemical mechanism of PFAS-CD interactions. These insights pave the way toward nanopore-based in situ detection with promises in environmental protection against PFAS pollution.

Drug-coated balloon (DCB) therapy is a promising endovascular treatment for obstructive arterial disease. The goal of DCB therapy is restoration of lumen patency in a stenotic vessel, whereby balloon deployment both mechanically compresses the offending lesion and locally delivers an antiproliferative drug, most commonly paclitaxel (PTX) or derivative compounds, to the arterial wall. Favorable long-term outcomes of DCB therapy thus require predictable and adequate PTX delivery, a process facilitated by coating excipients that promotes rapid drug transfer during the inflation period. While a variety of excipients have been considered in DCB design, there is a lack of understanding about the coating-specific biophysical determinants of essential device function, namely, acute drug transfer. We consider two hydrophilic excipients for PTX delivery, urea (UR) and poly(ethylene glycol) (PEG), and examine how compositional and preparational variables in the balloon surface spray-coating process impact resultant coating microstructure and in turn acute PTX transfer to the arterial wall. Specifically, we use scanning electron image analyses to quantify how coating microstructure is altered by excipient solid content and balloon-to-nozzle spray distance during the coating procedure and correlate obtained microstructural descriptors of coating aggregation to the efficiency of acute PTX transfer in a one-dimensional ex vivo model of DCB deployment. Experimental results suggest that despite the qualitatively different coating surface microstructures and apparent PTX transfer mechanisms exhibited with these excipients, the drug delivery efficiency is generally enhanced by coating aggregation on the balloon surface. We illustrate this microstructure-function relation with a finite element-based computational model of DCB deployment, which along with our experimental findings suggests a general design principle to increase drug delivery efficiency across a broad range of DCB designs.

Biotechnological innovations have vastly improved the capacity to perform large-scale protein studies, while the methods we have for identifying and quantifying individual proteins are still inadequate to perform protein sequencing at the single-molecule level. Nanopore-inspired systems devoted to understanding how single molecules behave have been extensively developed for applications in genome sequencing. These nanopore systems are emerging as prominent tools for protein identification, detection, and analysis, suggesting realistic prospects for novel protein sequencing. This review summarizes recent advances in biological nanopore sensors toward protein sequencing, from the identification of individual amino acids to the controlled translocation of peptides and proteins, with attention focused on device and algorithm development and the delineation of molecular mechanisms with the aid of simulations. Specifically, the review aims to offer recommendations for the advancement of nanopore-based protein sequencing from an engineering perspective, highlighting the need for collaborative efforts across multiple disciplines. These efforts should include chemical conjugation, protein engineering, molecular simulation, machine-learning-assisted identification, and electronic device fabrication to enable practical implementation in real-world scenarios.

Cytomegalovirus (CMV) is a member of the β-herpesviruses and is ubiquitous, infecting 50%-99% of the human population depending on ethnic and socioeconomic conditions. CMV establishes lifelong, latent infections in their host. Spontaneous reactivation of CMV is usually asymptomatic, but reactivation events in immunocompromised or immunosuppressed individuals can lead to severe morbidity and mortality. Moreover, herpesvirus infections have been associated with several cardiovascular and post-transplant diseases (stroke, atherosclerosis, post-transplant vasculopathy, and hypertension). Herpesviruses, including CMV, encode viral G-protein-coupled receptors (vGPCRs) that alter the host cell by hijacking signaling pathways that play important roles in the viral life cycle and these cardiovascular diseases. In this brief review, we discuss the pharmacology and signaling properties of these vGPCRs, and their contribution to hypertension. Overall, these vGPCRs can be considered attractive targets moving forward in the development of novel hypertensive therapies., (© The Author(s) 2023. Published by Oxford University Press on behalf of American Journal of Hypertension, Ltd. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Dementia refers to a particular group of symptoms characterized by difficulties with memory, language, problem-solving, and other thinking skills that affect a person's ability to perform everyday activities. Alzheimer's disease (AD) is the most common form of dementia, affecting about 6.2 million Americans aged 65 years and older. Likewise, cardiovascular diseases (CVDs) are a major cause of disability and premature death, impacting 126.9 million adults in the USA, a number that increases with age. Consequently, CVDs and cardiovascular risk factors are associated with an increased risk of AD and cognitive impairment. They share important age-related cardiometabolic and lifestyle risk factors, that make them among the leading causes of death. Additionally, there are several premises and hypotheses about the mechanisms underlying the association between AD and CVD. Although AD and CVD may be considered deleterious to health, the study of their combination constitutes a clinical challenge, and investigations to understand the mechanistic pathways for the cause-effect and/or shared pathology between these two disease constellations remains an active area of research. AD pathology is propagated by the amyloid β (Aβ) peptides. These peptides give rise to small, toxic, and soluble Aβ oligomers (SPOs) that are nonfibrillar, and it is their levels that show a robust correlation with the extent of cognitive impairment. This review will elucidate the interplay between the effects of accumulating SPOs in AD and CVDs, the resulting ER stress response, and their role in vascular dysfunction. We will also address the potential underlying mechanisms, including the possibility that SPOs are among the causes of vascular injury in CVD associated with cognitive decline. By revealing common mechanistic underpinnings of AD and CVD, we hope that novel experimental therapeutics can be designed to reduce the burden of these devastating diseases. Graphical abstract Alzheimer's disease (AD) pathology leads to the release of Aβ peptides, and their accumulation in the peripheral organs has varying effects on various components of the cardiovascular system including endoplasmic reticulum (ER) stress and vascular damage. Image created with BioRender.com., (© 2023. The Author(s), under exclusive licence to American Aging Association.)

We consider the thermal, mechanical, and chemical contact of two subsystems composed of ideal gases, both of which are not in the thermodynamic limit. After contact, the combined system is isolated, and the entropy is determined through the use of its standard connection to the phase space density (PSD), where only those microstates at a given energy value are counted. The various intensive properties of these small systems that follow from a derivative of the PSD, such as the temperature, pressure, and chemical potential (evaluated via a backward difference), while equal when the two subsystems are in equilibrium are nevertheless found not to behave in accordance with what is expected from macroscopic thermodynamics. Instead, it is the entropy, defined from its connection to the PSD, that still controls the behavior of these small (nonextensive) systems. We also analyze the contact of these two subsystems utilizing an alternative entropy definition, through its proposed connection to the phase space volume (PSV), where all microstates at or below a given energy value are counted. We show that certain key properties of these small systems obtained with the PSV either do not become equal or do not consistently describe the two subsystems when in contact, suggesting that the PSV should not be used for analyzing the behavior of small isolated systems.

Aqueous solvation free energies of adsorption have recently been measured for phenol adsorption on Pt(111). Endergonic solvent effects of ∼1 eV suggest solvents dramatically influence a metal catalyst's activity with significant implications for the catalyst design. However, measurements are indirect and involve adsorption isotherm models, which potentially reduces the reliability of the extracted energy values. Computational, implicit solvation models predict exergonic solvation effects for phenol adsorption, failing to agree with measurements even qualitatively. In this study, an explicit, hybrid quantum mechanical/molecular mechanical approach for computing solvation free energies of adsorption is developed, solvation free energies of phenol adsorption are computed, and experimental data for solvation free energies of phenol adsorption are reanalyzed using multiple adsorption isotherm models. Explicit solvation calculations predict an endergonic solvation free energy for phenol adsorption that agrees well with measurements to within the experimental and force field uncertainties. Computed adsorption free energies of solvation of carbon monoxide, ethylene glycol, benzene, and phenol over the (111) facet of Pt and Cu suggest that liquid water destabilizes all adsorbed species, with the largest impact on the largest adsorbates., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)

Developing tissues have intricate, three-dimensional (3D) organizations of cells and extracellular matrix (ECM) that provide the framework necessary to meet morphogenic and necessary demands. Migrating cells, in vivo, are exposed to numerous conflicting signals: chemokines, ECM, growth factors, and physical forces. While most of these have been studied individually in vivo or in vitro, our understanding of how cells integrate these various signals is lacking. We previously developed a novel self-organizing cellularized collagen hydrogel model that is adaptable, tunable, reproducible, and capable of mimicking the multitude of stimuli that cells experience. Our model produced self-assembled toroids of cells that were formed by 24 h. Data we present here show toroids initially form as early as 3 h after seeding. Additionally, toroids formed when cells were seeded on various collagen subtypes and were sensitive to the composition of the hydrogel. Moreover, we found differences in remodeling in toroid gels compared to gels with cells embedded in them using both a collagen binding peptide and rheology. Using scanning electron microscopy, we observed toroids forming a crater-like structure compared to whole gel contractions in mixed in gels. Finally, when multiple cells were mixed prior to seeding, heterogeneous toroids formed with some containing clusters of cells.

Modifications to the traditional Onsager theory for modeling isotropic-nematic phase transitions in hard prolate spheroidal systems are presented. Pure component systems are used to identify the need to update the Lee-Parsons resummation term. The Lee-Parsons resummation term uses the Carnahan-Starling equation of state to approximate higher-order virial coefficients beyond the second virial coefficient employed in Onsager's original theoretical approach. As more exact ways of calculating the excluded volume of two hard prolate spheroids of a given orientation are used, the division of the excluded volume by eight, which is an empirical correction used in the original Lee-Parsons resummation term, must be replaced by six to yield a better match between the theoretical and simulation results. These modifications are also extended to binary mixtures of hard prolate spheroids using the Boublík-Mansoori-Carnahan-Starling-Leland (BMCSL) equation of state.

Background: Mouse models of abdominal aortic aneurysm (AAA) and dissection have proven to be invaluable in the advancement of diagnostics and therapeutics by providing a platform to decipher response variables that are elusive in human populations. One such model involves systemic Angiotensin II (Ang-II) infusion into low density-lipoprotein receptor-deficient (LDLr-/-) mice leading to intramural thrombus formation, inflammation, matrix degradation, dilation, and dissection. Despite its effectiveness, considerable experimental variability has been observed in AAAs taken from our Ang-II infused LDLr-/- mice (n=12) with obvious dissection occurring in 3 samples, outer bulge radii ranging from 0.73 to 2.12 mm, burst pressures ranging from 155 to 540 mmHg, and rupture location occurring 0.05 to 2.53 mm from the peak bulge location., Objective: We hypothesized that surface curvature, a fundamental measure of shape, could serve as a useful predictor of AAA failure at supra-physiological inflation pressures., Methods: To test this hypothesis, we fit well-known biquadratic surface patches to 360° micro-mechanical test data and used Spearman's rank correlation (rho) to identify relationships between failure metrics and curvature indices., Results: We found the strongest associations between burst pressure and the maximum value of the first principal curvature (rho=-0.591, p-val=0.061), the maximum value of Mean curvature (rho=-0.545, p-val=0.087), and local values of Mean curvature at the burst location (rho=-0.864, p-val=0.001) with only the latter significant after Bonferroni correction. Additionally, the surface profile at failure was predominantly convex and hyperbolic (saddle-shaped) as indicated by a negative sign in the Gaussian curvature. Findings reiterate the importance of shape in experimental models of AAA.

Biological membranes have distinct geometries that confer specific functions. However, the molecular mechanisms underlying the phenomenological geometry/function correlations remain elusive. We studied the effect of membrane geometry on the localization of membrane-bound proteins. Quantitative comparative experiments between the two most abundant cellular membrane geometries, spherical and cylindrical, revealed that geometry regulates the spatial segregation of proteins. The measured geometry-driven segregation reached 50-fold for membranes of the same mean curvature, demonstrating a crucial and hitherto unaccounted contribution by Gaussian curvature. Molecular-field theory calculations elucidated the underlying physical and molecular mechanisms. Our results reveal that distinct membrane geometries have specific physicochemical properties and thus establish a ubiquitous mechanistic foundation for unravelling the conserved correlations between biological function and membrane polymorphism., Competing Interests: The authors declare no competing financial interest., (Copyright © 2020 American Chemical Society.)

Nanoparticles (NPs) constitute a powerful therapeutic platform with exciting prospects as potential inhibitors of amyloid-[Formula: see text] (Aβ) aggregation, a process associated with Alzheimer's disease (AD). Researchers have synthesized and tested a large collection of NPs with disparate sizes, shapes, electrostatic properties and surface ligands that evoke a variety of responses on Aβ aggregation. In spite of a decade of research on the NP-Aβ system and many promising experimental results, NPs have failed to progress to any level of clinical trials for AD. A theoretical framework with which to approach this physical system is presented featuring two simple metrics, (1) the extent to which NPs adsorb Aβ, and (2) the degree to which interaction with a NP alters Aβ conformation relative to aggregation propensity. Most of our current understanding of these two interactions has been gained through experimentation, and many of these studies are reviewed herein. We also provide a potential roadmap for studies that we believe could produce viable NPs as an effective AD therapeutic platform.

The performance of aptamer-based biosensors is crucially impacted by their interactions with physiological metal ions, which can alter their structures and chemical properties. Therefore, elucidating the nature of these interactions carries the utmost importance in the robust design of highly efficient biosensors. We investigated Mg 2 + binding to varying sequences of polymers to capture the effects of ionic strength and grafting density on ion binding and molecular reorganization of the polymer layer. The polymers are modeled as ssDNA aptamers using a self-consistent field theory, which accounts for non-covalent ion binding by integrating experimentally-derived binding constants. Our model captures the typical polyelectrolyte behavior of chain collapse with increased ionic strength for the ssDNA chains at low grafting density and exhibits the well-known re-entrant phenomena of stretched chains with increased ionic strength at high grafting density. The binding results suggest that electrostatic attraction between the monomers and Mg 2 + plays the dominant role in defining the ion cloud around the ssDNA chains and generates a nearly-uniform ion distribution along the chains containing varying monomer sequences. These findings are in qualitative agreement with recent experimental results for Mg 2 + binding to surface-bound ssDNA.

Amyloid-β (Aβ) protein aggregates through a complex pathway to progress from monomers to soluble oligomers and ultimately insoluble fibrils. Because of the dynamic nature of aggregation, it has proven exceedingly difficult to determine the precise interactions that lead to the formation of transient oligomers. Here, a statistical thermodynamic model has been developed to elucidate these interactions. Aβ 1-42 was simulated using fully atomistic replica exchange molecular dynamics. We use an ensemble of approximately 5 × 10 5 configurations taken from simulation as input in a self-consistent field theory that explicitly accounts for the size, shape, and charge distribution of both the amino acids comprising Aβ and all molecular species present in solution. The solution of the model equations provides a prediction of the probabilities of the configurations of the Aβ dimer and the potential of mean force between two monomers during the dimerization process. This model constitutes a reliable methodology to elucidate the underlying physics of the Aβ dimerization process as a function of pH, temperature, and salt concentration. The results obtained with this new model could be valuable in the design of Aβ oligomerization inhibitors, a prospective therapeutic for Alzheimer's disease.

An aortic aneurysm (AA) is a focal dilatation of the aortic wall. Occurrence of AA rupture is an all too common event that is associated with high levels of patient morbidity and mortality. The decision to surgically intervene prior to AA rupture is made with recognition of significant procedural risks, and is primarily based on the maximal diameter and/or growth rate of the AA. Despite established thresholds for intervention, rupture occurs in a notable subset of patients exhibiting sub-critical maximal diameters and/or growth rates. Therefore, a pressing need remains to identify better predictors of rupture risk and ultimately integrate their measurement into clinical decision making. In this study, we use a series of finite element-based computational models that represent a range of plausible AA scenarios, and evaluate the relative sensitivity of wall stress to geometrical and mechanical properties of the aneurysmal tissue. Taken together, our findings encourage an expansion of geometrical parameters considered for rupture risk assessment, and provide perspective on the degree to which tissue mechanical properties may modulate peak stress values within aneurysmal tissue.

Proteins anchored to membranes through covalently linked fatty acids and/or isoprenoid groups play crucial roles in all forms of life. Sorting and trafficking of lipidated proteins has traditionally been discussed in the context of partitioning to membrane domains of different lipid composition. We recently showed that membrane shape/curvature can in itself mediate the recruitment of lipidated proteins. However, exactly how membrane curvature and composition synergize remains largely unexplored. Here we investigated how three critical structural parameters of lipids, namely acyl chain saturation, headgroup size, and acyl chain length, modulate the capacity of membrane curvature to recruit lipidated proteins. As a model system we used the lipidated minimal membrane anchor of the GTPase, N-Ras (tN-Ras). Our data revealed complex synergistic effects, whereby tN-Ras binding was higher on planar DOPC than POPC membranes, but inversely higher on curved POPC than DOPC membranes. This variation in the binding to both planar and curved membranes leads to a net increase in the recruitment by membrane curvature of tN-Ras when reducing the acyl chain saturation state. Additionally, we found increased recruitment by membrane curvature of tN-Ras when substituting PC for PE, and when decreasing acyl chain length from 14 to 12 carbons (DMPC versus DLPC). However, these variations in recruitment ability had different origins, with the headgroup size primarily influencing tN-Ras binding to planar membranes whereas the change in acyl chain length primarily affected binding to curved membranes. Molecular field theory calculations recapitulated these findings and revealed lateral pressure as an underlying biophysical mechanism dictating how curvature and composition synergize to modulate recruitment of lipidated proteins. Our findings suggest that the different compositions of cellular compartments could modulate the potency of membrane curvature to recruit lipidated proteins and thereby synergistically regulate the trafficking and sorting of lipidated proteins., (Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Background: Deposits of aggregated amyloid-β protein (Aβ) are a pathological hallmark of Alzheimer's disease (AD). Thus, one therapeutic strategy is to eliminate these deposits by halting Aβ aggregation. While a variety of possible aggregation inhibitors have been explored, only nanoparticles (NPs) exhibit promise at low substoichiometric ratios. With tunable size, shape, and surface properties, NPs present an ideal platform for rationally designed Aβ aggregation inhibitors. In this study, we characterized the inhibitory capabilities of gold nanospheres exhibiting different surface coatings and diameters., Results: Both NP diameter and surface chemistry were found to modulate the extent of aggregation, while NP electric charge influenced aggregate morphology. Notably, 8 nm and 18 nm poly(acrylic acid)-coated NPs abrogated Aβ aggregation at a substoichiometric ratio of 1:2,000,000. Theoretical calculations suggest that this low stoichiometry could arise from altered solution conditions near the NP surface. Specifically, local solution pH and charge density are congruent with conditions that influence aggregation., Conclusions: These findings demonstrate the potential of surface-coated gold nanospheres to serve as tunable therapeutic agents for the inhibition of Aβ aggregation. Insights gained into the physiochemical properties of effective NP inhibitors will inform future rational design of effective NP-based therapeutics for AD.

Coronary artery bypass grafting (CABG) acutely disturbs the homeostatic state of the transplanted vessel making retention of graft patency dependent on chronic remodeling processes. The time course and extent to which remodeling restores vessel homeostasis will depend, in part, on the nature and magnitude of the mechanical disturbances induced upon transplantation. In this investigation, biaxial mechanical testing and histology were performed on the porcine left anterior descending artery (LAD) and analogs of common autografts, including the internal thoracic artery (ITA), radial artery (RA), great saphenous vein (GSV) and lateral saphenous vein (LSV). Experimental data were used to quantify the parameters of a structure-based constitutive model enabling prediction of the acute vessel mechanical response pre-transplantation and under coronary loading conditions. A novel metric Ξ was developed to quantify mechanical differences between each graft vessel in situ and the LAD in situ, while a second metric Ω compares the graft vessels in situ to their state under coronary loading. The relative values of these metrics among candidate autograft sources are consistent with vessel-specific variations in CABG clinical success rates with the ITA as the superior and GSV the inferior graft choices based on mechanical performance. This approach can be used to evaluate other candidate tissues for grafting or to aid in the development of synthetic and tissue engineered alternatives., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Using microscopic molecular theory, we determine the bending and saddle-splay constants of three-component lipid bilayers. The membrane contains cholesterol, dipalmitoyl-phosphatidylcholine (DPPC) and dioleoylphosphatidylcholine (DOPC) and the predictions of the theory have been shown to qualitatively reproduce phase diagrams of giant unilamellar vesicles (GUVs) of the same three components. The bending and saddle-splay constants were calculated for the gel, liquid-ordered (lo) and liquid-disordered (ld) phases. By proper expansion of the free energy, the molecular theory enables us to determine the effects of the mode of membrane bending deformation on the value of the elastic constants for different phases. In particular, we refer to the ability of the molecules to arrange the composition between the two monolayers upon deformation. The bending and saddle-splay constants obtained from the free energy expansion can be expressed in terms of moments of the local lateral pressures and their derivatives, all evaluated for a symmetric planar bilayer. The effect of blocked vs. free exchange of lipids across the two monolayers on the values of the bending constant is as high as 50 k(B)Tin the ld phase to as high as 200 k(B)T in the lo phase. These results show that one must strongly consider the mode of deformation in determining the mechanical properties of lipid bilayers. We discuss how the different contributions to the lateral pressures affect the values of the elastic constants, including the effects of the cholesterol concentration and temperature on the membrane elastic constants. We also calculate the equilibrium binding concentrations of lipid tail anchors as a function of membrane curvature by explicitly determining the chemical potential difference of species across a curved bilayer. Our results are in excellent agreement with recent experimental results.

Given the proposed importance of membrane tension in regulating cellular functions, we explore the effects of a finite surface tension on phase equilibrium using a molecular theory that captures the quantitative structure of the phase diagram of the tensionless DPPC/DOPC/Cholesterol lipid bilayer. We find that an increase in the surface tension decreases the temperature of the transition from liquid to gel in a pure DPPC system by ∼1.0 K/(mN/m), and decreases the liquid-disordered to liquid-ordered transition at constant chemical potentials by approximately the same amount. Our results quantitatively isolate the role of tension in comparison to other thermodynamic factors, such as pressure, in determining the phase behavior of lipid bilayers., (Copyright © 2012 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

Charge regulation in polyacid monolayers attached at one end to a planar surface is studied theoretically. The polyacid layers are designed to mimic single-stranded DNA monolayers. The effects of the local pH and salt concentration on the protonation states of the polyacid layer are studied using a molecular mean-field theory that includes a microscopic description of the conformations of the polyacid molecule along with electrostatic interactions, acid-base equilibrium, and excluded volume interactions. We predict that, in the case of a monovalent salt, NaCl, the amount of proton binding increases dramatically for high surface coverage of polyacid and low bulk salt concentration. When the polyelectrolyte is almost completely charge neutralized by bound protons, there is an expulsion of sodium from the layer. We show that the degree of protonation can go all the way from 0% to 100% when the bulk pH is kept fixed at 7 by changing the surface coverage of polyacid and the bulk salt concentration. The effects of increasing protonation and the expulsion of the cations from the monolayer are reduced when sodium ions are replaced by divalent magnesium ions. Our theoretical results concur with X-ray photoelectron spectroscopy studies of ssDNA monolayers on gold., (© 2011 American Chemical Society)

There is clear evidence of an interleaflet coupling in model lipid/cholesterol membranes exhibiting liquid-liquid phase separation. The strength of this coupling is quantified by the mismatch free energy, γ. We calculate it using a molecular mean-field model of a phase-separated lipid/cholesterol bilayer and obtain values that increase as the concentration of saturated lipids in the coexisting phases is increased. These values lie in the range 0.01-0.03 k(B)T/nm(2). We clarify the relationship between the interleaflet coupling and the extent of interleaflet alignment of liquid domains by analyzing a statistical mechanical model of coupled fluctuating domain interfaces. The model is solved exactly using the correspondence between statistical mechanics and quantum mechanics, yielding an expression for the characteristic size of fluctuations out of domain registry. This length scale depends only weakly on the strength of the interleaflet coupling and inevitably is only of the order of nanometers, which explains the experimental result that fluctuations out of domain registry have not been observed by optical microscopy., (Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

The free energy of forming a droplet and a bubble with a given particle number n and volume v within the pure-component Lennard-Jones supercooled vapor and superheated liquid, respectively, are further explored using density-functional theory. Similar to what was found previously [M. J. Uline and D. S. Corti, Phys. Rev. Lett. 99, 076102 (2007); M. J. Uline and D. S. Corti, J. Chem. Phys. 129, 234507 (2008)], the limits of stability again appear within both free energy surfaces evaluated at two other metastability conditions, one closer to the binodal and one closer to the spinodal. Furthermore, an ad hoc bond connectivity criterion is also applied in an attempt, however approximately, to eliminate certain configurational redundancies that arise from the chosen droplet and bubble definitions. What results are free energy surfaces describing the formation of equilibrium embryos that should be an improved representation of the fluctuations that are relevant to those nonequilibrium embryos seen in an actual nucleation event. Finally, we discuss in some detail the use of the (n,v) reaction coordinate within the framework of an equilibrium-based theory and its relation to other descriptions of nucleation.

The free energy of forming a droplet and a bubble with a given number of particles n inside a volume v within the pure component Lennard-Jones supercooled vapor and superheated liquid, respectively, is further explored using density-functional theory. Certain key aspects of the free energy surface for bubble formation, such as the radius of the bubble at a stability limit, are found to scale in a nearly temperature independent manner when plotted versus a parameter that quantifies the location of the given state point in the metastable region. The corresponding work at this stability limit exhibits scaling for small values of n, but shows a strong temperature dependence for large n. No aspect of the free energy surface for droplet formation shows scaling over the full range of metastability conditions, including the work of forming the critical droplet and the radius of a droplet at its stability limit. Hence, there is no "universal" surface for embryo formation in metastable fluids. We also generate by thermodynamic arguments alone droplet and bubble trajectories along the corresponding free energy surfaces that avoid by construction the locus of instabilities, which match quite well the results obtained from other approaches. We also discuss in greater detail the use of the (n,v) order parameter within an equilibrium-based description of embryo formation, focusing on why the density profile of the embryo is found to be discontinuous at the embryo surface and why stability limits are expected to develop at certain bubble radii.

We calculate partition coefficients of various chain anchors in liquid-ordered and liquid-disordered phases utilizing a theoretical model of a bilayer membrane containing cholesterol, dipalmitoyl phosphatidylcholine, and dioleoylphosphatidylcholine. The partition coefficients are calculated as a function of chain length, degree of saturation, and temperature. Partitioning depends on the difference between the lipid environments of the coexisting phases in which the anchors are embedded. Consequently, the partition coefficient depends on the nature of the anchor, and on the relative compositions of the coexisting phases. We find that saturated anchors prefer the denser liquid-ordered phase, and that the fraction of anchors in the liquid-ordered phase increases with increasing degree of saturation of the anchors. The partition coefficient also depends upon the location of the double bonds. Anchors with double bonds closer to the middle of the chain have a greater effect on partitioning than those near the end. Doubling the number of saturated chains increases the partitioning into the liquid-ordered phase for tails that are nearly as long or longer than those comprising the bilayer. Partitioning of such chains increases with decreasing temperature, indicating that energy considerations dominate entropic ones. In contrast, partitioning of shorter chains increases with increasing temperature, indicating that entropic considerations dominate., (Copyright (c) 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.)

For the pure-component supercooled Lennard-Jones vapor, the free energy of forming a droplet with a given particle number and volume is calculated using density-functional theory. In contrast to what was noted in previous studies, the free energy surface beyond the pseudosaddle point no longer exhibits a valley but rather channels the nuclei toward a locus of instabilities, initiating an unstable growth phase. Similar to a previous study of bubble formation in superheated liquids [M. J. Uline and D. S. Corti, Phys. Rev. Lett. 99, 076102 (2007)], a new picture of homogeneous droplet nucleation and growth emerges.

Based on the approach of Gruhn and Monson [Phys. Rev. E 63, 061106 (2001)], we present a new method for deriving the collisions dynamics for particles that interact via discontinuous potentials. By invoking the conservation of the extended Hamiltonian, we generate molecular dynamics (MD) algorithms for simulating the hard-sphere and square-well fluids within the isothermal-isobaric (NpT) ensemble. Consistent with the recent rigorous reformulation of the NpT ensemble partition function, the equations of motion impose a constant external pressure via the introduction of a shell particle of known mass [M. J. Uline and D. S. Corti, J. Chem. Phys. 123, 164101 (2005); 123, 164102 (2005)], which serves to define uniquely the volume of the system. The particles are also connected to a temperature reservoir through the use of a chain of Nose-Hoover thermostats, the properties of which are not affected by a hard-sphere or square-well collision. By using the Liouville operator formalism and the Trotter expansion theorem to integrate the equations of motion, the update of the thermostat variables can be decoupled from the update of the positions of the particles and the momentum changes upon a collision. Hence, once the appropriate collision dynamics for the isobaric-isenthalpic (NpH) equations of motion is known, the adaptation of the algorithm to the NpT ensemble is straightforward. Results of MD simulations for the pure component square-well fluid are presented and serve to validate our algorithm. Finally, since the mass of the shell particle is known, the system itself, and not a piston of arbitrary mass, controls the time scales for internal pressure and volume fluctuations. We therefore consider the influence of the shell particle algorithm on the dynamics of the square-well fluid.

We consider various ensemble averages within the molecular dynamics (MD) ensemble, corresponding to those states sampled during a MD simulation in which the application of periodic boundary conditions imposes a constraint on the momentum of the center of mass. As noted by Shirts et al. [J. Chem. Phys. 125, 164102 (2006)] for an isolated system, we find that the principle of equipartition is not satisfied within such simulations, i.e., the total kinetic energy of the system is not shared equally among all the translational degrees of freedom. Nevertheless, we derive two different versions of Tolman's generalized equipartition theorem, one appropriate for the canonical ensemble and the other relevant to the microcanonical ensemble. In both cases, the breakdown of the principle of equipartition immediately follows from Tolman's result. The translational degrees of freedom are, however, still equivalent, being coupled to the same bulk property in an identical manner. We also show that the temperature of an isolated system is not directly proportional to the average of the total kinetic energy (in contrast to the direct proportionality that arises between the temperature of the external bath and the kinetic energy within the canonical ensemble). Consequently, the system temperature does not appear within Tolman's generalized equipartition theorem for the microcanonical ensemble (unlike the immediate appearance of the temperature of the external bath within the canonical ensemble). Both of these results serve to highlight the flaws in the argument put forth by Hertz [Ann. Phys. 33, 225 (1910); 33, 537 (1910)] for defining the entropy of an isolated system via the integral of the phase space volume. Only the Boltzmann-Planck entropy definition, which connects entropy to the integral of the phase space density, leads to the correct description of the properties of a finite, isolated system. We demonstrate that the use of the integral of the phase space volume leads to unphysical results, indicating that the property of adiabatic invariance has little to do with the behavior of small systems.

For the superheated Lennard-Jones liquid, the free energy of forming a bubble with a given particle number and volume is calculated using density-functional theory. As conjectured, a consequence of known properties of the critical cavity [S. N. Punnathanam and D. S. Corti, J. Chem. Phys. 119, 10 224 (2003), the free energy surface terminates at a locus of instability. These stability limits reside, however, unexpectedly close to the saddle point. A new picture of homogeneous bubble nucleation and growth emerges from our study, being more appropriately described as an "activated instability."

The results of a series of constant pressure and temperature molecular-dynamics (MD) simulation studies based on the rigorous shell particle formulation of the isothermal-isobaric (NpT) ensemble are presented. These MD simulations validate the newly proposed constant pressure equations of motion in which a "shell" particle is used to define uniquely the volume of the system [M. J. Uline and D. S. Corti, J. Chem. Phys. (to be published), preceding paper]. Ensemble averages obtained with the new MD NpT algorithm match the ensemble averages obtained using the previously derived shell particle Monte Carlo NpT method [D. S. Corti, Mol. Phys. 100, 1887 (2002)]. In addition, we also verify that the Hoover NpT MD algorithm [W. G. Hoover, Phys. Rev. A 31, 1695 (1985); 34, 2499 (1986)] generates the correct ensemble averages, though only when periodic boundary conditions are employed. The extension of the shell particle MD algorithm to multicomponent systems is also discussed, in which we show for equilibrium properties that the identity of the shell particle is completely arbitrary when periodic boundary conditions are applied. Self-diffusion coefficients determined with the shell particle equations of motion are also identical to those obtained in other ensembles. Finally, since the mass of the shell particle is known, the system itself, and not a piston of arbitrary mass, controls the time scales for internal pressure and volume fluctuations. We therefore consider the effects of the shell particle on the dynamics of the system. Overall, the shell particle MD algorithm is an effective simulation method for studying systems exposed to a constant external pressure and may provide an advantage over other existing constant pressure approaches when developing nonequilibrium MD methods.

Current constant pressure molecular-dynamics (MD) algorithms are not consistent with the recent reformulation of the isothermal-isobaric (NpT) ensemble. The NpT ensemble partition function requires the use of a "shell" molecule to identify uniquely the volume of the system, thereby avoiding the redundant counting of configurations [e.g., G. J. M. Koper and H. Reiss, J. Phys. Chem. 100, 422 (1996); D. S. Corti, Phys. Rev. E, 64, 016128 (2001)]. So far, only the NpT Monte Carlo method has been updated to allow the system volume to be defined by a shell particle [D. S. Corti, Mol. Phys. 100, 1887 (2002)]. A shell particle has yet to be incorporated into MD simulations. The proper modification of the NpT MD algorithm is therefore the subject of this paper. Unlike Andersen's method [H. C. Andersen, J. Chem. Phys. 72, 2384 (1980)] where a piston of unknown mass serves to control the response time of volume fluctuations, the newly proposed equations of motion impose a constant external pressure via the introduction of a shell particle of known mass. Hence, the system itself sets the time scales for pressure and volume fluctuations. The new algorithm is subject to a number of fundamentally rigorous tests to ensure that the equations of motion sample phase space correctly. We also show that the Hoover NpT algorithm [W. G. Hoover, Phys. Rev. A. 31, 1695 (1985); 34, 2499 (1986)] does sample phase correctly, but only when periodic boundary conditions are employed.