Biomedical subjects
Publications and source records attributed to Peter G Bolhuis.
We report molecular simulations suggesting that the kinetics of surfactant micelle formation can be sped up significantly by a replication mechanism, in which growing micelles become unstable and split into two similar sized micelles. We argue that for certain surfactants types around the critical micelle concentration, such a mechanism becomes more dominant than the commonly accepted nucleation pathway.
We perform grand-canonical molecular simulations to study the molecular mechanism of clay swelling hysteresis as a function of the relative humidity. In particular, we focus on the transition from the one- to the two-layer hydrate and the influence of three types of counterions (Li+, Na+, and K+). Our results cover the experimental relative humidity region where swelling and shrinking usually occur. We show that the thermodynamic origin of swelling hysteresis is a free-energy barrier separating the layered hydrates. This free-energy barrier is dominated by breaking and formation of hydrogen bonds between and within water layers. This network of water molecules is similar for all counterions, but the positions of these counterions depend upon their size. The relatively large K+ counterions show more affinity for clay surface adsorption, which increases the free-energy barrier and inhibits swelling. On the other hand, the relatively small Li+ counterions are quite well-accommodated in the water network, and thereby, they can form a new swelling state with a basal spacing of approximately 13.5 A. This new swelling state is an alternative explanation for the widely accepted simultaneous occurrence of two or more swelling phases.
We determine the free energy of micelle formation for surfactants in a solvent by employing a hybrid semi-grand Monte Carlo simulation scheme in combination with umbrella sampling and configurational bias techniques. We compare results of two surfactant models: one based on Lennard-Jones interactions and one based on the soft repulsive potential that is often used in dissipative particle dynamics (DPD). The free energies of micellization in both models show similar behavior. However, although the critical micelle concentration for the Lennard-Jones systems lies within the experimental range, it is 13 orders of magnitude lower for the soft repulsive model. We discuss the implication for the applicability of soft repulsive potentials for the study of micelle formation.
We study the kinetics of crystal nucleation of an undercooled Lennard-Jones liquid using various path-sampling methods. We obtain the rate constant and elucidate the pathways for crystal nucleation. Analysis of the path ensemble reveals that crystal nucleation occurs along many different pathways, in which critical solid nuclei can be small, compact, and face centered cubic, but also large, less ordered, and more body centered cubic. The reaction coordinate thus includes, besides the cluster size, also the quality of the crystal structure.
We introduce a method to evaluate simultaneously the reaction rate constant and the free energy profile of a process in a complex environment. The method employs the partial path transition interface sampling technique we recently developed for the calculation of rate constants in diffusive systems. We illustrate the applicability of the technique by studying a simple dimer in a repulsive fluid, and show that the free energy can be obtained at no additional computational cost.
We determine the free energy of micelle formation for model surfactants in a Lennard-Jones solvent by employing a hybrid semi-grand Monte Carlo simulation scheme in combination with umbrella sampling and configurational bias techniques. Comparing the results to theoretical prediction, we obtain good agreement for large micellar sizes. We also study the effect of changing the surfactant headgroup size and tail length on the critical micelle concentration. The values of and the trends in the calculated critical micelle concentrations do agree with experimental observation for nonionic surfactants. The results open up the way for the calculation of critical micelle concentrations using realistic atomic force fields.
As a bacterial blue light sensor the photoactive yellow protein (PYP) undergoes conformational changes upon signal transduction. The absorption of a photon triggers a series of events that are initially localized around the protein chromophore, extends to encompass the whole protein within microseconds, and leads to the formation of the transient pB signaling state. We study the formation of this signaling state pB by molecular simulation and predict its solution structure. Conventional straightforward molecular dynamics is not able to address this formation process due to the long (microsecond) timescales involved, which are (partially) caused by the presence of free energy barriers between the metastable states. To overcome these barriers, we employed the parallel tempering (or replica exchange) method, thus enabling us to predict qualitatively the formation of the PYP signaling state pB. In contrast to the receptor state pG of PYP, the characteristics of this predicted pB structure include a wide open chromophore-binding pocket, with the chromophore and Glu(46) fully solvent-exposed. In addition, loss of alpha-helical structure occurs, caused by the opening motion of the chromophore-binding pocket and the disruptive interaction of the negatively charged Glu(46) with the backbone atoms in the hydrophobic core of the N-terminal cap. Recent NMR experiments agree very well with these predictions.
We examine the dynamical (un)folding pathways of the C-terminal beta-hairpin of protein G-B1 at room temperature in explicit solvent, by employing transition path sampling algorithms. The path ensembles contain information on the folding kinetics, including solvent motion. We determine the transition state ensembles for the two main transitions: 1), the hydrophobic collapse; and 2), the backbone hydrogen bond formation. In both cases the transition state ensembles are characterized by a layer (1) or a strip (2) of water molecules in between the two hairpin strands, supporting the hypothesis of the solvent as lubricant in the folding process. The transition state ensembles do not correspond with saddle points in the equilibrium free-energy landscapes. The kinetic pathways are thus not completely determined by the free-energy landscape. This phenomenon can occur if the order parameters obey different timescales. Using the transition interface sampling technique, we calculate the rate constants for (un)folding and find them in reasonable agreement with experiments, thus supporting the validation of using all-atom force fields to study protein folding.
We introduce a path sampling method for the computation of rate constants for complex systems with a highly diffusive character. Based on the recently developed transition interface sampling (TIS) algorithm this procedure increases the efficiency by sampling only parts of complete transition trajectories. The algorithm assumes the loss of memory for diffusive progression along the reaction coordinate. We compare the new partial path technique to the TIS method for a simple diatomic system and show that the computational effort of the new method scales linearly, instead of quadratically, with the width of the diffusive barrier. The validity of the memory loss assumption is also discussed.
We examine the dynamical folding pathways of the C-terminal beta-hairpin of protein G-B1 in explicit solvent at room temperature by means of a transition-path sampling algorithm. In agreement with previous free-energy calculations, the resulting path ensembles reveal a folding mechanism in which the hydrophobic residues collapse first followed by backbone hydrogen-bond formation, starting with the hydrogen bonds inside the hydrophobic core. In addition, the path ensembles contain information on the folding kinetics, including solvent motion. Using the recently developed transition interface sampling technique, we calculate the rate constant for unfolding of the protein fragment and find it to be in reasonable agreement with experiments. The results support the validation of using all-atom force fields to study protein folding.
We computed the phase-separation behavior and effective interactions of colloid-polymer mixtures in the "protein limit," where the polymer radius of gyration is much larger than the colloid radius. For ideal polymers, the critical colloidal packing fraction tends to zero, whereas for interacting polymers in a good solvent the behavior is governed by a universal binodal, implying a constant critical colloid packing fraction. In both systems the depletion interaction is not well described by effective pair potentials but requires the incorporation of many-body contributions.
This article reviews the concepts and methods of transition path sampling. These methods allow computational studies of rare events without requiring prior knowledge of mechanisms, reaction coordinates, and transition states. Based upon a statistical mechanics of trajectory space, they provide a perspective with which time dependent phenomena, even for systems driven far from equilibrium, can be examined with the same types of importance sampling tools that in the past have been applied so successfully to static equilibrium properties.