Reduced variance analysis of molecular dynamics simulations by linear combination of estimators.

Building upon recent developments of force-based estimators with a reduced variance for the computation of densities, radial distribution functions, or local transport properties from molecular simulations, we show that the variance can be further reduced by considering optimal linear combinations of such estimators. This control variates approach, well known in statistics and already used in other branches of computational physics, has been comparatively much less exploited in molecular simulations. We illustrate this idea on the radial distribution function and the one-dimensional density of a bulk and confined Lennard-Jones fluid, where the optimal combination of estimators is determined for each distance or position, respectively. In addition to reducing the variance everywhere at virtually no additional cost, this approach cures an artifact of the initial force-based estimators, namely, small but non-zero values of the quantities in regions where they should vanish. Beyond the examples considered here, the present work highlights, more generally, the underexplored potential of control variates to estimate observables from molecular simulations.

Insulin-degrading enzyme higher in subjects with metabolic syndrome.

Metabolic syndrome (MS) is comprised of a cluster of abnormalities in glucose, lipid, and vascular homeostasis, which is most commonly linked to abdominal obesity. MS heralds increased risk for development of diabetes and is linked to impairment in insulin signaling. Insulin-degrading enzyme (IDE) is one of the mechanisms through which insulin blood levels are maintained. It has been previously suggested that controlling IDE levels could provide yet another potential therapeutic approach in diabetes. Here we aim to investigate whether changes in serum IDE levels correlate with the severity of MS. Using a highly sensitive ELISA assay of active IDE in human serum, we found a strong correlation between circulating IDE levels and circulating levels of triglycerides, insulin, and c-peptide and an inverse correlation with HDL cholesterol (HDLc). Serum IDE levels were higher in MS subjects than in control subjects. Hence, circulating IDE may serve as a tool to identify subjects with abnormal insulin metabolism, possibly those with MS that are at risk to develop diabetes.

Studying polymer diffusiophoresis with non-equilibrium molecular dynamics.

We report a numerical study of the diffusiophoresis of short polymers using non-equilibrium molecular dynamics simulations. More precisely, we consider polymer chains in a fluid containing a solute that has a concentration gradient and examine the variation of the induced diffusiophoretic velocity of the polymer chains as the interaction between the monomer and the solute is varied. We find that there is a non-monotonic relation between the diffusiophoretic mobility and the strength of the monomer-solute interaction. In addition, we find a weak dependence of the mobility on the length of the polymer chain, which shows clear difference from the diffusiophoresis of a solid particle. Interestingly, the hydrodynamic flow through the polymer is much less screened than for pressure driven flows.

Addressing hysteresis and slow equilibration issues in cavity-based calculation of chemical potentials.

In this paper, we explore the strengths and weaknesses of a cavity-based method to calculate the excess chemical potential of a large molecular solute in a dense liquid solvent. Use of the cavity alleviates some technical problems associated with the appearance of (integrable) divergences in the integrand during alchemical particle growth. The excess chemical potential calculated using the cavity-based method should be independent of the cavity attributes. However, the performance of the method (equilibration time and the robustness) does depend on the cavity attributes. To illustrate the importance of a suitable choice of the cavity attributes, we calculate the partition coefficient of pyrene in toluene and heptane using a coarse-grained model. We find that a poor choice for the functional form of the cavity may lead to hysteresis between growth and shrinkage of the cavity. Somewhat unexpectedly, we find that, by allowing the cavity to move as a pseudo-particle within the simulation box, the decay time of fluctuations in the integrand of the thermodynamic integration can be reduced by an order of magnitude, thereby increasing the statistical accuracy of the calculation.

Theoretical Prediction of Thermal Polarization.

We present a mean-field theory to explain the thermo-orientation effect in an off-center Stockmayer fluid. This effect is the underlying cause of thermally induced polarization and thermally induced monopoles, which have recently been predicted theoretically. Unlike previous theories that are based either on phenomenological equations or on scaling arguments, our approach does not require any fitting parameters. Given an equation of state and assuming local equilibrium, we construct an effective Hamiltonian for the computation of local Boltzmann averages. This simple theoretical treatment predicts molecular orientations that are in very good agreement with simulation results for the range of dipole strengths investigated. By decomposing the overall alignment into contributions from the temperature and density gradients, we shed further light on how the nonequilibrium result arises from the competition between the two gradients.

Non-equilibrium simulations of thermally induced electric fields in water.

Using non-equilibrium molecular dynamics simulations, it has been recently demonstrated that water molecules align in response to an imposed temperature gradient, resulting in an effective electric field. Here, we investigate how thermally induced fields depend on the underlying treatment of long-ranged interactions. For the short-ranged Wolf method and Ewald summation, we find the peak strength of the field to range between 2 × 10(7) and 5 × 10(7) V/m for a temperature gradient of 5.2 K/Å. Our value for the Wolf method is therefore an order of magnitude lower than the literature value [J. A. Armstrong and F. Bresme, J. Chem. Phys. 139, 014504 (2013); J. Armstrong et al., J. Chem. Phys. 143, 036101 (2015)]. We show that this discrepancy can be traced back to the use of an incorrect kernel in the calculation of the electrostatic field. More seriously, we find that the Wolf method fails to predict correct molecular orientations, resulting in dipole densities with opposite sign to those computed using Ewald summation. By considering two different multipole expansions, we show that, for inhomogeneous polarisations, the quadrupole contribution can be significant and even outweigh the dipole contribution to the field. Finally, we propose a more accurate way of calculating the electrostatic potential and the field. In particular, we show that averaging the microscopic field analytically to obtain the macroscopic Maxwell field reduces the error bars by up to an order of magnitude. As a consequence, the simulation times required to reach a given statistical accuracy decrease by up to two orders of magnitude.

An enhanced version of the heat exchange algorithm with excellent energy conservation properties.

We propose a new algorithm for non-equilibrium molecular dynamics simulations of thermal gradients. The algorithm is an extension of the heat exchange algorithm developed by Hafskjold et al. [Mol. Phys. 80, 1389 (1993); 81, 251 (1994)], in which a certain amount of heat is added to one region and removed from another by rescaling velocities appropriately. Since the amount of added and removed heat is the same and the dynamics between velocity rescaling steps is Hamiltonian, the heat exchange algorithm is expected to conserve the energy. However, it has been reported previously that the original version of the heat exchange algorithm exhibits a pronounced drift in the total energy, the exact cause of which remained hitherto unclear. Here, we show that the energy drift is due to the truncation error arising from the operator splitting and suggest an additional coordinate integration step as a remedy. The new algorithm retains all the advantages of the original one whilst exhibiting excellent energy conservation as illustrated for a Lennard-Jones liquid and SPC/E water.

Brain MRI of nasal MOG therapeutic effect in relapsing-progressive EAE.

Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system (CNS) considered to be a T cell-mediated autoimmune disease. Mucosally administered antigens induce regulatory T cells that secrete anti-inflammatory cytokines at the anatomic site where the mucosally administered Ag is located. We have previously reported in a mouse model of stroke that nasal treatment with MOG35-55 peptide reduces ischemic infarct size and improves behavior, by inducing IL-10-secreting T cells. We have also demonstrated that an experimental autoimmune encephalomyelitis (EAE) model in non-obese diabetic (NOD) mice leads to a relapsing progressive disease and that brain lesions can be visualized noninvasively by magnetic resonance imaging (MRI). Here, we investigated whether nasal treatment with 25µg of MOG35-55 after the first attack affects clinical progression and MRI outcome in the NOD model. We found that nasal MOG35-55 treatment administered three times after the first attack and then weekly reduced both the peak clinical disease score and clinical score during remission. Pathology revealed less infiltration of cells and reduction in white-matter damage as measured by Luxol blue staining in treated animals. This model is unique in that there are lesions in the corpus callosum, external capsule, fimbria, internal capsule and thalamus, which is analogous to what is observed in MS. MRI of individual animals using fractional anisotropy (FA) and T1-gadolinum (T1-Gd) imaging was able to identify lesions in all of these anatomic areas, and we found lower levels of brain pathology by MRI in treated mice with both methods. Our results indicate a beneficial effect of nasal MOG on relapsing-progressive EAE and demonstrate that non-invasive MRI imaging may be used to monitor treatment of ongoing disease in this model for testing new therapies for MS.

Living clusters and crystals from low-density suspensions of active colloids.

Recent studies aimed at investigating artificial analogs of bacterial colonies have shown that low-density suspensions of self-propelled particles confined in two dimensions can assemble into finite aggregates that merge and split, but have a typical size that remains constant (living clusters). In this Letter, we address the problem of the formation of living clusters and crystals of active particles in three dimensions. We study two systems: self-propelled particles interacting via a generic attractive potential and colloids that can move toward each other as a result of active agents (e.g., by molecular motors). In both cases, fluidlike "living" clusters form. We explain this general feature in terms of the balance between active forces and regression to thermodynamic equilibrium. This balance can be quantified in terms of a dimensionless number that allows us to collapse the observed clustering behavior onto a universal curve. We also discuss how active motion affects the kinetics of crystal formation.

Naphthoquinone-tyrptophan reduces neurotoxic Aß*56 levels and improves cognition in Alzheimer's disease animal model.

An increasing body of evidence indicates a role for oligomers of the amyloid-ß peptide (Aß) in the neurotoxicity of this peptide and the pathology of Alzheimer's disease (AD). Several neurotoxic oligomeric forms of Aß have been noted ranging from the larger Amyloid ß-Derived Diffusible Ligands (ADDLs) to smaller trimers and dimers of Aß. More recently a dodecameric form of Aß with a 56 kDa molecular weight, denoted Aß*56, was shown to cause memory impairment in AD model mice. Here, we present for the first time a potential therapeutic strategy for AD that targets the early stages in the formation of neurotoxic Aß*56 oligomers using a modified quinone-Tryptophan small molecule N-(3-chloro-1,4-dihydro-1,4-dioxo-2-naphthalenyl)-L-Tryptophan (Cl-NQTrp). Using NMR spectroscopy we show that this compound binds the aromatic recognition core of Aß and prevents the formation of oligomers. We assessed the effect of Cl-NQTrp in vivo in transgenic flies expressing Aß(1-42) in their nervous system. When these flies were fed with Cl-NQTrp a marked alleviation of their Aß-engendered reduced life span and defective locomotion was observed. Finally, intraperitoneal injection of Cl-NQTrp into an aggressive AD mouse model reduced the level of the Aß*56 species in their brain and reversed their cognitive defects. Further experiments should assess whether this is a direct effect of the drug in the brain or an indirect peripheral effect. This is the first demonstration that targeted reduction of Aß*56 results in amelioration of AD symptoms. This second generation of tryptophan-modified naphthoquinones could therefore serve as potent disease modifying therapeutic for AD.

Simulation of nucleation in almost hard-sphere colloids: the discrepancy between experiment and simulation persists.

In this paper we examine the phase behavior of the Weeks-Chandler-Andersen (WCA) potential with ßε = 40. Crystal nucleation in this model system was recently studied by Kawasaki and Tanaka [Proc. Natl. Acad. Sci. U.S.A. 107, 14036 (2010)], who argued that the computed nucleation rates agree well with experiment, a finding that contradicted earlier simulation results. Here we report an extensive numerical study of crystallization in the WCA model, using three totally different techniques (Brownian dynamics, umbrella sampling, and forward flux sampling). We find that all simulations yield essentially the same nucleation rates. However, these rates differ significantly from the values reported by Kawasaki and Tanaka and hence we argue that the huge discrepancy in nucleation rates between simulation and experiment persists. When we map the WCA model onto a hard-sphere system, we find good agreement between the present simulation results and those that had been obtained for hard spheres [L. Filion, M. Hermes, R. Ni, and M. Dijkstra, J. Chem. Phys. 133, 244115 (2010); S. Auer and D. Frenkel, Nature 409, 1020 (2001)].

Characterization of brain lesions in a mouse model of progressive multiple sclerosis.

Multiple sclerosis (MS) is an autoimmune disease of the central nervous system characterized by damage to the neuronal myelin sheath, which results in different levels of muscle paralysis that can lead to neuronal death. In most MS mouse models, the neurologic damage mostly affects the spinal cord with limited damage to the brain, which cannot be monitored by magnetic resonance imaging (MRI) as used for humans. We show that immunization of non-obese diabetic (NOD) mice with myelin oligodendrocyte glycoprotein peptide 35-55 leads to the development of relapsing-remitting stages, evident from days 20 to 70, which then develops into a chronic progressive stage. This cycle is similar to MS stages found in humans. Brain MRI gadolinium-enhanced T1-weighted image analysis showed an increased blood-brain barrier permeability in brain gray and white matter specific to the corpus callosum, fimbria, and internal capsule as found in humans. MRI fractional anisotropy analysis showed demyelination and axonal damage in identical regions. Immunohistologic analysis supported the MRI data. No evidence of brain lesions was found in a common model of MS using C57BL/6 mice. We suggest that an increase in astrocyte toxicity in experimental autoimmune encephalomyelitis-induced NOD mice may be linked to brain lesion development. We suggest using NOD mice as a suitable model for studying MS using MRI methods toward future diagnostic and drug development.

Recent advances in the modelling and simulation of electrokinetic effects: bridging the gap between atomistic and macroscopic descriptions.

Electrokinetic phenomena are of great practical importance in fields as diverse as micro-fluidics, colloid science and oil exploration. However, the quantitative prediction of electrokinetic effects was until recently limited to relatively simple geometries that allowed the use of analytical theories. In the past decade, there has been a rapid development in the use of numerical methods that can be used to model electrokinetic phenomena in complex geometries or, more generally, under conditions where the existing analytical approaches fail. The present paper discusses these recent developments, with special emphasis on the advent of coarse-grained models that make it possible to bridge the gap between a purely atomistic and macroscopic descriptions.

Free-energy-based method for step size detection of processive molecular motors.

We report a free-energy-based algorithm to estimate the step size of processive molecular motors from noisy, experimental time position traces. In our approach, the problem of estimating step sizes reduces to the evaluation of the free energy of directed lattice polymers in a random potential. The present approach is Bayesian in spirit as we do not aim to determine the most likely underlying time trace but rather to determine the step size and stepping frequency that are most likely to yield the observed data. We test this method on synthetic data for the simple case of noisy traces with fixed underlying step size and Poissonian stepping statistics. We find that the present scheme can work at signal-to-noise levels that are about 40% worse than those where the best existing step detection methods fail. More importantly, the present approach yields a much more accurate estimate of the step size. Although we focus on the case of non-reversing walks with a single step size, we show that we can detect if this assumption is violated. In principle, the method can be extended to more complex stepping scenarios but we find that for noisy data, multi-parameter fits are not reliable.

Induction and regulation of Trypanosoma brucei VSG-specific antibody responses.

The review addresses how infection with Trypanosoma brucei affects the development, survival and functions of B lymphocytes in mice. It discusses (1) the contributions of antibodies to trypanosome clearance from the bloodstream, (2) how B lymphocytes, the precursors of antibody producing plasma cells, interact with membrane form variable surface glycoprotein (VSG), i.e. with monovalent antigen that is free to diffuse within the lipid bilayer of the trypanosome plasma membrane and consequently can cross-link B cell antigen specific receptors by indirect processes only and (3) the extent and underlying causes of dysregulation of humoral immune responses in infected mice, focusing on the impact of wild type and GPI-PLC⁻/⁻ trypanosomes on bone marrow and extramedullary B lymphopoiesis, B cell maturation and survival.

Geometrical frustration: a study of four-dimensional hard spheres.

The smallest maximum-kissing-number Voronoi polyhedron of three-dimensional (3D) Euclidean spheres is the icosahedron, and the tetrahedron is the smallest volume that can show up in Delaunay tessellation. No periodic lattice is consistent with either, and hence these dense packings are geometrically frustrated. Because icosahedra can be assembled from almost perfect tetrahedra, the terms "icosahedral" and "polytetrahedral" packing are often used interchangeably, which leaves the true origin of geometric frustration unclear. Here we report a computational study of freezing of 4D Euclidean hard spheres, where the densest Voronoi cluster is compatible with the symmetry of the densest crystal, while polytetrahedral order is not. We observe that, under otherwise comparable conditions, crystal nucleation in four dimensions is less facile than in three dimensions, which is consistent with earlier observations [M. Skoge, Phys. Rev. E 74, 041127 (2006)]. We conclude that it is the geometrical frustration of polytetrahedral structures that inhibits crystallization.

Field-induced self-assembly of suspended colloidal membranes.

We report experiments that probe the self-assembly of micrometer-size colloids into one-particle-thick, robust, and self-healing membranes. In a magic-angle precessing magnetic field, superparamagnetic spheres experience isotropic pair attraction similar to the van der Waals force between atoms. But the many-body polarization interactions among them steer an ordered aggregation pathway consisting of growth of short chains, cross-linking and network formation, network coarsening, and consolidation of membrane patches. This generic aggregation scenario can be induced in any particles of large enough susceptibility.

Two-step vapor-crystal nucleation close below triple point.

We present the results of Monte Carlo simulations of crystal nucleation from the vapor phase. We studied the Lennard-Jones system at conditions close to, but below, the triple point. This system is expected to show surface melting. The nucleation pathway that we observe consists of two distinct steps. In the first step, a liquid droplet nucleates from the vapor. Its nucleation rate depends strongly on the vapor supersaturation. In the second step, the final crystal phase nucleates in the liquid droplet, provided that this liquid droplet exceeds a minimum size. Our simulations show that within a liquid droplet the crystal nucleation rate does not depend on the vapor supersaturation. In a recent independent study Chen et al. [J. Phys. Chem. B 112, 4069 (2008)] investigated the same phenomenon using umbrella sampling to compute free energy barriers and hence nucleation rates. We use a different numerical approach where we focus on computing the nucleation rates directly using forward-flux sampling. Our results agree with the findings of Chen et al. and both methods observe two-step nucleation. This finding indicates that this nucleation process can be described with a quasiequilibrium theory. Due to different cutoffs for the interaction potential the results cannot be compared quantitatively.

Neuroprotective and neurotoxic properties of glial cells in the pathogenesis of Alzheimer's disease.

Alzheimer's disease (AD) affects more than 18 million people worldwide and is characterized by progressive memory deficits, cognitive impairment and personality changes. The main cause of AD is generally attributed to the increased production and accumulation of amyloid-beta (Abeta), in association with neurofibrillary tangle (NFT) formation. Increased levels of pro-inflammatory factors such as cytokines and chemokines, and the activation of the complement cascade occurs in the brains of AD patients and contributes to the local inflammatory response triggered by senile plaque. The existence of an inflammatory component in AD is now well known on the basis of epidemiological findings showing a reduced prevalence of the disease upon long-term medication with anti-inflammatory drugs, and evidence from studies of clinical materials that shows an accumulation of activated glial cells, particularly microglia and astrocytes, in the same areas as amyloid plaques. Glial cells maintain brain plasticity and protect the brain for functional recovery from injuries. Dysfunction of glial cells may promote neurodegeneration and, eventually, the retraction of neuronal synapses, which leads to cognitive deficits. The focus of this review is on glial cells and their diversity properties in AD.

Irreducible finite-size effects in the surface free energy of NaCl crystals from crystal-nucleation data.

In this Letter we report a simulation study in which we compare the solid-liquid interfacial free energy of NaCl at coexistence, gamma_{LS}, with the value that follows from the height of the homogeneous nucleation barrier. The two estimates differ by more than 100%. Smaller discrepancies are found for gamma_{LS} of hard-sphere and of Lennard-Jones particles. We consider a variety of possible causes for this discrepancy and conclude that it is due to a finite-size effect that cannot be corrected for by any simple thermodynamic procedure. By taking into account the finite-size effects of gamma_{LS} obtained in real nucleation experiments, we obtain quantitative agreement between gamma_{LS} estimated in the simulations and derived from the experiments. Our finding suggests that most published solid-liquid surface free energies derived from nucleation experiments will have to be revised.