Biomedical subjects

D Frenkel

Publications and source records attributed to D Frenkel.

At least 19 recordsLinked to original sources

PubMed2004

Onset of heterogeneous crystal nucleation in colloidal suspensions.

The addition of small 'seed' particles to a supersaturated solution can greatly increase the rate at which crystals nucleate. This process is understood, at least qualitatively, when the seed has the same structure as the crystal that it spawns. However, the microscopic mechanism of seeding by a 'foreign' substance is not well understood. Here we report numerical simulations of colloidal crystallization seeded by foreign objects. We perform Monte Carlo simulations to study how smooth spherical seeds of various sizes affect crystallization in a suspension of hard colloidal particles. We compute the free-energy barrier associated with crystal nucleation. A low barrier implies that nucleation is easy. We find that to be effective crystallization promoters, the seed particles need to exceed a well-defined minimum size. Just above this size, seed particles act as crystallization 'catalysts' as newly formed crystallites detach from the seed. In contrast, larger seed particles remain covered by the crystallites that they spawn. This phenomenon should be experimentally observable and can have important consequences for the control of the resulting crystal size distribution.

Journal Article↗

PubMed2004

Simulation study of intra- and intermicellar ordering in triblock-copolymer systems.

We report a numerical study of the structure and phase behavior of a model for a triblock-copolymer solution. The aim of this study is to investigate the nature of the dense micellar phase that can form in such systems. The simulations were performed on a lattice model for PEO (poly(ethylene-oxide))-PPO (poly(propylene-oxide))-PEO polymers. At high volume fractions, the structure factor of the amphiphile-solvent system can be mapped onto that of a monodisperse hard-sphere fluid. Yet, a low-density hard-sphere model cannot account for the properties of the dilute micellar solution. Moreover, direct inspection of the snapshots of the suspension show that these model triblock-copolymer micelles are neither hard, nor spherical, nor monodisperse.

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PubMed2004

Numerical prediction of absolute crystallization rates in hard-sphere colloids.

Special computational techniques are required to compute absolute crystal nucleation rates of colloidal suspensions. Using crystal nucleation of hard-sphere colloids as an example, we describe in some detail the novel computational tools that are needed to perform such calculations. In particular, we focus on the definition of appropriate order parameters that distinguish liquid from crystal, and on techniques to compute the kinetic prefactor that enters in the expression for the nucleation rate. In addition, we discuss the relation between simulation results and theoretical predictions based on classical nucleation theory.

Journal Article↗

PubMed2004

Multiple stalk formation as a pathway of defect-induced membrane fusion.

We propose that the first stage of membrane fusion need not be the formation of a single stalk. Instead, we consider a scenario for defect-induced membrane fusion that proceeds cooperatively via multiple stalk formation. The defects (stalks or pores) attract each other via membrane-mediated capillary interactions that result in a condensation transition of the defects. The resulting dense phase of stalks corresponds to the so-called fusion intermediate.

Cell Membrane↗

PubMed2003

Designing refoldable model molecules.

We report a numerical study of the design of lattice heteropolymers that can refold when the properties of only a few monomers are changed. If we assume that the effect of an external agent on a heteropolymer is to alter the interactions between its constituent monomers, our simulations provide a description of a simple allosteric transition. We characterize the free energy surfaces of the initial and the modified chain molecule. We find that there is a region of conformation space where molecules can be made to refold with minimal free energy cost. This region is accessible by thermal fluctuations. The efficiency of a motor based on such an allosteric transition would be enhanced by "borrowing" heat from the environment in the initial stages of the refolding, and "paying back" later. In fact, the power cycle of many real molecular motors does involve such a borrowing activation step.

Journal Article↗

PubMed2003

Line tension controls wall-induced crystal nucleation in hard-sphere colloids.

We report on a numerical study of the effect of a smooth, hard wall on the crystallization of hard-sphere colloids. We find that the presence of the wall drastically lowers the barrier for crystal nucleation, but it does not eliminate it. Crystal nucleation becomes noticeable at pressures that are some 5% above the coexistence value. The first particles to crystallize on the wall form a (111) plane. Initially, this crystallite grows laterally, rather than in the third dimension. The free energy of the critical crystal nucleus on the wall is about 2 orders of magnitudes lower than in the bulk. Analysis of the numerical data indicates that, at coexistence, the (111) plane is at the threshold of wetting the wall. The nucleation barrier is dominated by line tension.

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PubMed2003

Phase behavior and crystallization kinetics of poly-12-hydroxystearic-coated polymethylmethacrylate colloids.

Polymethylmethacrylate (PMMA) colloids sterically stabilized by a layer of chemically grafted poly-12-hydroxystearic (PHSA) are widely used in experiments as model hard spheres. However, due to the coating, the interaction between particles is slightly soft. Here we report a numerical study of the effect of the PHSA coating on the phase behavior and crystallization kinetics of PMMA colloids based on parameters determined from surface-force measurements on PHSA-PMMA-coated mica surfaces [B. A. de L. Costello and P. F. Luckham, J. Colloid Interface Sci. 156, 72 (1993); B. A. de L. Costello et al., Langmuir 8, 464 (1992)]. We find that the core volume fraction of particles at freezing measured by Pusey and van Megen [Nature 320, 340 (1986)] can only be reproduced by using a thickness of the PHSA layer that is considerably larger than literature values. This may indicate that the particles are in fact slightly charged. Compared to perfect hard spheres, the crystallization rate in these slightly soft particles was found to be increased by about two orders of magnitudes.

Journal Article↗

PubMed2002

Generation and brain delivery of anti-aggregating antibodies against beta-amyloid plaques using phage display technology.

Antibodies towards the N-terminal region of the beta-amyloid peptide bind to beta-amyloid fibrils, leading to their disaggregation. We generated anti-aggregating beta-amyloid antibodies using filamentous phages displaying the only four amino acids EFRH found to be the main regulatory site for beta-amyloid formation. In order to overcome the low permeability of the blood brain barrier for targeting 'anti-aggregating' mAbs to the betaA plaques in the brain, we applied antibody engineering methods to minimize the size of the mAbs while maintaining their biological activity. We found that single-chain antibodies displayed on the surface of the phage are capable of entering the central nervous system (CNS). The feasibility of these novel strategies for the production and targeting of anti-aggregating antibodies against beta-amyloid plaques to disease affected regions in the CNS may have clinical potential for treatment of Alzheimer's disease.

Alzheimer Disease↗

PubMed2001

Lattice-Boltzmann method for the simulation of transport phenomena in charged colloids.

We present a simulation scheme based on the lattice-Boltzmann method to simulate the dynamics of charged colloids in an electrolyte. In our model we describe the electrostatics on the level of a Poisson-Boltzmann equation and the hydrodynamics of the fluid by the linearized Navier-Stokes equations. We verify our simulation scheme by means of a Chapman-Enskog expansion. Our method is applied to the calculation of the reduced sedimentation velocity U/U(0) for a cubic array of charged spheres in an electrolyte. We show that we recover the analytical solution first derived by Booth [F. Booth, J. Chem. Phys. 22, 1956 (1954)] for a weakly charged, isolated sphere in an unbounded electrolyte. The present method makes it possible to go beyond the Booth theory, and we discuss the dependence of the sedimentation velocity on the charge of the spheres. Finally we compare our results to experimental data.

Journal Article↗

PubMed2001

Suppression of crystal nucleation in polydisperse colloids due to increase of the surface free energy.

The formation of small crystallites is governed by two competing factors: the free energy gained upon transferring constituent atoms, molecules or colloidal particles from the metastable liquid to the more stable solid, and the free energy needed to create the surface area of the crystallite. Because the ratio of surface area to bulk is large for small particles, small crystallites dissolve spontaneously under conditions where larger crystallites are stable and macroscopic crystal growth occurs only if spontaneously formed crystallites exceed a critical minimum size. On theoretical grounds, the probability of forming such critical crystal nuclei is expected to increase rapidly with supersaturation. However, experiments show that the rate of crystal nucleation in many systems goes through a maximum as the supersaturation is increased. It is commonly assumed that the nucleation rate peaks because, even though the probability of forming critical nuclei increases with increasing concentration, the rate of growth of such nuclei decreases. Here we report simulations of crystal nucleation in suspensions of colloidal spheres with varying size distributions that show that the probability that critical nuclei will form itself goes through a maximum as the supersaturation is increased. We find that this effect, which is strongest for systems with the broadest particle size distribution, results from an increase with supersaturation of the solid-liquid interfacial free energy. The magnitude of this effect suggests that vitrification at high supersaturations should yield colloidal glasses that are truly amorphous, rather than nano-crystalline.

Journal Article↗

PubMed2001

Generation of auto-antibodies towards Alzheimer's disease vaccination.

We developed a novel procedure to evoke anti-aggregating beta-amyloid (Abeta) antibodies, using filamentous phages displaying only four amino acids EFRH of the beta-amyloid peptide (AbetaP). This epitope was found to be the main regulatory site for fibril formation. For the first time, effective auto-antibodies have been obtained in guinea-pigs, which exhibit human identity in the AbetaP. Immunization through a phage-carrying epitope was found to be long-lasting, and no toxic effect caused by autoimmune response was detected in the challenged animal sections. These antibodies performed similarly to site-directed monoclonal antibodies and to antibodies raised against fibrillar Abeta in disaggregation of plaques, and may serve as the basis for developing an anti-Abeta vaccine.

Alzheimer Disease↗

PubMed2001

Prediction of absolute crystal-nucleation rate in hard-sphere colloids.

Crystal nucleation is a much-studied phenomenon, yet the rate at which it occurs remains difficult to predict. Small crystal nuclei form spontaneously in supersaturated solutions, but unless their size exceeds a critical value--the so-called critical nucleus--they will re-dissolve rather than grow. It is this rate-limiting step that has proved difficult to probe experimentally. The crystal nucleation rate depends on Pcrit, the (very small) probability that a critical nucleus forms spontaneously, and on a kinetic factor (kappa) that measures the rate at which critical nuclei subsequently grow. Given the absence of a priori knowledge of either quantity, classical nucleation theory is commonly used to analyse crystal nucleation experiments, with the unconstrained parameters adjusted to fit the observations. This approach yields no 'first principles' prediction of absolute nucleation rates. Here we approach the problem from a different angle, simulating the nucleation process in a suspension of hard colloidal spheres, to obtain quantitative numerical predictions of the crystal nucleation rate. We find large discrepancies between the computed nucleation rates and those deduced from experiments: the best experimental estimates of Pcrit seem to be too large by several orders of magnitude.

Journal Article↗

PubMed2000

Immunization against Alzheimer's beta -amyloid plaques via EFRH phage administration.

The epitope EFRH, corresponding to amino acids 3-6 within the human beta-amyloid peptide (AbetaP), acts as a regulatory site controlling both the formation and disaggregation process of the beta-amyloid fibrils (Abeta). Locking of this epitope by highly specific antibodies affects the dynamics of the entire AbetaP molecule, preventing self-aggregation as well as enabling resolubilization of already formed aggregates. Production of such antibodies by repeated injections of toxic human Abeta fibrils into transgenic mice suggests the feasibility of vaccination against Alzheimer's disease. Here, we report the development of an immunization procedure for the production of effective anti-aggregating beta-amyloid antibodies based on filamentous phages displaying the EFRH peptide as specific and nontoxic antigen. Effective autoimmune antibodies were obtained by EFRH phage administration in guinea pigs, which exhibit AbetaP identical to the human AbetaP region. Moreover, because of the high antigenicity of the phage, no adjuvant is required to obtain high affinity anti-aggregating IgG antibodies after a short immunization period of 3 weeks. Availability of such antibodies opens up possibilities for the development of an efficient and long-lasting vaccination for the prevention and treatment of Alzheimer's disease.

Alzheimer Disease↗

PubMed2000

Modulation of Alzheimer's beta-amyloid neurotoxicity by site-directed single-chain antibody.

A single-chain antibody was constructed from variable regions of heavy and light genes of the parental anti-beta-amyloid peptide IgM 508 antibody. This antibody exhibits anti-aggregating properties, leading to disaggregation of Alzheimer beta-amyloid (betaA) fibrils and prevents its toxic effect on cultured PC-12 cells. Sequencing of the small antibody, namely 508 (Fv), revealed that the V(L) domain contained a cysteine residue in the complementary determining region (CDR)3 (residue 96) which affects its solubility and stability. The cysteine codon was replaced using SOE PCR, and one of the mutants obtained, namely 508F(Fv) (containing phenylalanine instead of cysteine), showed an increased storage stability and higher affinity compared to the wild type. Antibody 508F(Fv) prevents the neurotoxicity of betaA (90% cell viability) and disrupts the fibril structure of beta-amyloid (62% decrease in ThT fluorescence). The ability of antibody 508F(Fv) to dissolve already-formed betaA fibrils makes it a good candidate for intracellular expression and modulation of APP processing as the first step towards the production of therapeutic protection molecules for Alzheimer's disease treatment.

Alzheimer Disease↗

PubMed2000

Influence of vacancies on the melting transition of hard disks in two dimensions

We present the results of molecular dynamics simulations of two-dimensional (2D) hard disk systems in the vicinity of melting. The simulations are used to calculate the elastic constants, which can be used to estimate the location of the Kosterlitz-Thouless dislocation unbinding transition. Simulations on defect-free lattices indicate that this transition is expected to occur at essentially the same density as a first-order solid-isotropic transition and so it is not possible to rule out either a one step weak first-order transition between the solid and the isotropic fluid or a two step transition via a hexatic phase. Simulations performed on systems with vacancies indicate that the elastic constants are essentially unchanged at constant density. This result implies that vacancies have little influence on the melting of 2D hard disk solids.

Journal Article↗

PubMed2000

Enhanced stability of layered phases in parallel hard spherocylinders due to addition of hard spheres

There is increasing evidence that entropy can induce microphase separation in binary fluid mixtures interacting through hard particle potentials. One such phase consists of alternating two-dimensional liquidlike layers of rods and spheres. We study the transition from a uniform miscible state to this ordered state using computer simulations, and compare results to experiments and theory. We conclude the following: (1) There is stable entropy driven microphase separation in mixtures of parallel rods and spheres. (2) Adding spheres smaller than the rod length decreases the total volume fraction needed for the formation of a layered phase, and therefore small spheres effectively stabilize the layered phase; the opposite is true for large spheres. (3) The degree of this stabilization increases with increasing rod length.

Journal Article↗

PubMed2000

Phase behavior of model mixtures of colloidal disks and polymers

The phase behavior of model colloidal systems containing platelets and polymer is investigated using computer simulation and perturbation theory. For polymer coils with a diameter sigma(P) larger than 0.3sigma(D), where sigma(D) is the diameter of the platelets, isotropic fluid-fluid coexistence is observed, in addition to the usual isotropic-nematic transition for hard disk systems. For very small polymer coils (sigma(P)<0.1sigma(D)), a nematic-nematic demixing transition is observed, although this occurs at extremely high platelet density. The case of colloidal platelets and thin stiff rods is also examined. Demixing is observed in the isotropic phase for long rods and in the nematic phase for short rods, as for large and small polymer coils, respectively. However, the nematic-nematic demixing transition for platelet-rod mixtures occurs at a much lower platelet density than in the platelet-disk mixtures.

Journal Article↗

PubMed2000

Vaccination for the prevention and treatment of Alzheimer's disease.

In vitro studies showed that beta-amyloid peptide neurotoxicity correlates with the formation of fibrillar beta-amyloid and the variation in neurotoxic potency is related to the extent of peptide aggregation. Many efforts are being focused on the development of potent and selective inhibitors of amyloid formation in order to reduce the extent of their deposition and related neurotoxic effects. In our laboratory we are pioneering the idea that site-directed monoclonal antibodies (MAbs) can solubilize synthetic beta-amyloid aggregates. Production and performance of such antibodies by repeated injections of toxic human beta-amyloid fibrils into transgenic mice suggests the feasibility of vaccination against Alzheimer's disease (AD). Here we report the development of a novel immunization procedure for the production of effective antiaggregating beta-amyloid antibodies. The antigen is built from filamentous phages displaying the only four amino acids EFRH located at positions 3-6 of the beta-amyloid peptide found to be the main regulatory site of amyloid formation. Autoimmune antibodies are obtained by EFRH phage administration in guinea pigs, which exhibit human identity in the beta-amyloid peptide region. Availability of such antibodies opens up possibilities for the development of an efficient and long-lasting immunization procedure for the treatment of AD.

Journal Article↗