Stochastic Molecular Dynamics Simulations Research Articles

H-Bonds in Crambin: Coherence in an α-Helix.

We applied coherence analysis-used by engineers to identify linear interactions in stochastic systems-to molecular dynamics simulations of crambin, a thionin storage protein found in Abyssinian cabbage. A key advantage of coherence over other analyses is that it is robust, independent of the properties, or even the existence of probability distributions often relied on in statistical mechanics. For frequencies between 0.391 and 5.08 GHz (corresponding reciprocally to times of 2.56 and 0.197 ns), the displacements of oxygen and nitrogen atoms across α-helix H-bonds are strongly correlated, with a coherence greater than 0.9; the secondary structure causes the H-bonds to effectively act as a spring. Similar coherence behavior is observed for covalent bonds and other noncovalent interactions including H-bonds in β-sheets and salt bridges. In contrast, arbitrary pairs of atoms that are physically distant have uncorrelated motions and negligible coherence. These results suggest that coherence may be used to objectively identify atomic interactions without subjective thresholds such as H-bond lengths angles and angles. Strong coherence is also observed between the average position of adjacent leaves (groups of atoms) in an α-helix, suggesting that the harmonic analysis of classical molecular dynamics can successfully describe the propagation of allosteric interactions through the structure.

Stochastic simulation of nonequilibrium heat conduction in extended molecular junctions.

Understanding phononic heat transport processes in molecular junctions is a central issue in the developing field of nanoscale heat conduction. Here, we present a Langevin dynamics simulation framework to investigate heat transport processes in molecular junctions at and beyond the linear response regime and apply it to saturated and unsaturated linear hydrocarbon chains connecting two gold substrates. Thermal boundary conditions represented by Markovian noise and damping are filtered through several (up to four) gold layers to provide a realistic and controllable bath spectral density. Classical simulations using the full universal force field are compared with quantum calculations that use only the harmonic part of this field. The close agreement found at about room temperature between these very different calculations suggests that heat transport at such temperatures is dominated by lower frequency vibrations whose dynamics is described well by classical mechanics. The results obtained for alkanedithiol molecules connecting gold substrates agree with previous quantum calculations based on the Landauer formula and match recent experimental measurements [e.g., thermal conductance around 20 pW/K for alkanedithiols in single-molecule junctions (SMJs)]. Heat conductance simulations on polyynes of different lengths illuminate the effects of molecular conjugation on thermal transport. The difference between alkanes and polyynes is not large but correlates with the larger rigidity and stronger mode localization that characterize the polyyne structure. This computational approach has been recently used [R. Chen, I. Sharony, and A. Nitzan, J. Phys. Chem. Lett. 11, 4261-4268 (2020)] to unveil local atomic heat currents and phononic interference effect in aromatic-ring based SMJs.

Structural effects and competition mechanisms targeting the interactions between p53 and MDM2 for cancer therapy

Approximately half of all human cancers show normal TP53 gene expression but aberrant overexpression of MDM2 and/or MDMX. This fact suggests a promising cancer therapeutic strategy in targeting the interactions between p53 and MDM2/MDMX. To help realize the goal of developing effective inhibitors to disrupt the p53–MDM2/MDMX interaction, we systematically investigated the structural and interaction characteristics of p53 with inhibitors of its interactions with MDM2 and MDMX from an atomistic perspective using stochastic molecular dynamics simulations. We found that some specific α helices in the structures of MDM2 and MDMX play key roles in their binding to inhibitors, and that the hydrogen bond formed by the Trp23 residue of p53 with its counterpart in MDM2 or MDMX determines the dynamic competition processes of the disruption of the MDM2–p53 interaction and replacement of p53 from the MDM2–p53 complex in vivo. The results reported in this paper are expected to provide basic information for designing functional inhibitors and realizing new strategies of cancer gene therapy.

Pore translocation of knotted DNA rings

We use an accurate coarse-grained model for DNA and stochastic molecular dynamics simulations to study the pore translocation of 10-kbp-long DNA rings that are knotted. By monitoring various topological and physical observables we find that there is not one, as previously assumed, but rather two qualitatively different modes of knot translocation. For both modes the pore obstruction caused by knot passage has a brief duration and typically occurs at a late translocation stage. Both effects are well in agreement with experiments and can be rationalized with a transparent model based on the concurrent tensioning and sliding of the translocating knotted chains. We also observed that the duration of the pore obstruction event is more controlled by the knot translocation velocity than the knot size. These features should advance the interpretation and design of future experiments aimed at probing the spontaneous knotting of biopolymers.

Direct prediction of residual dipolar couplings of small molecules in a stretched gel by stochastic molecular dynamics simulations.

Residual dipolar couplings are highly useful NMR parameters for calculating and refining molecular structures, dynamics, and interactions. For some applications, however, it is inevitable that the preferred orientation of a molecule in an alignment medium is calculated a priori. Several methods have been developed to predict molecular orientations and residual dipolar couplings. Being beneficial for macromolecules and selected small-molecule applications, such approaches lack sufficient accuracy for a large number of organic compounds for which the fine structure and eventually the flexibility of all involved molecules have to be considered or are limited to specific, well-studied liquid crystals. We introduce a simplified model for detailed all-atom molecular dynamics calculations with a polymer strand lined up along the principal axis as a new approach to simulate the preferred orientation of small to medium-sized solutes in polymer-based, gel-type alignment media. As is shown by a first example of strychnine in a polystyrene/CDCl3 gel, the simulations potentially enable the accurate prediction of residual dipolar couplings taking into account structural details and dynamic averaging effects of both the polymer and the solute.

Structure-affinity properties of a high-affinity ligand of FKBP12 studied by molecular simulations of a binding intermediate.

With a view to explaining the structure-affinity properties of the ligands of the protein FKBP12, we characterized a binding intermediate state between this protein and a high-affinity ligand. Indeed, the nature and extent of the intermolecular contacts developed in such a species may play a role on its stability and, hence, on the overall association rate. To find the binding intermediate, a molecular simulation protocol was used to unbind the ligand by gradually decreasing the biasing forces introduced. The intermediate was subsequently refined with 17 independent stochastic boundary molecular dynamics simulations that provide a consistent picture of the intermediate state. In this state, the core region of the ligand remains stable, notably because of the two anchoring oxygen atoms that correspond to recurrent motifs found in all FKBP12 ligand core structures. Besides, the non-core regions participate in numerous transient intermolecular and intramolecular contacts. The dynamic aspect of most of the contacts seems important both for the ligand to retain at least a part of its configurational entropy and for avoiding a trapped state along the binding pathway. Since the transient and anchoring contacts contribute to increasing the stability of the intermediate, as a corollary, the dissociation rate constant of this intermediate should be decreased, resulting in an increase of the affinity constant . The present results support our previous conclusions and provide a coherent rationale for explaining the prevalence in high-affinity ligands of (i) the two oxygen atoms found in carbonyl or sulfonyl groups of dissimilar core structures and of (ii) symmetric or pseudo-symmetric mobile groups of atoms found as non-core moieties. Another interesting aspect of the intermediate is the distortion of the flexible 80 s loop of the protein, mainly in its tip region, that promotes the accessibility to the bound state.

Diffusion within the Cytoplasm: A Mesoscale Model of Interacting Macromolecules

Recent experiments carried out in the dense cytoplasm of living cells have highlighted the importance of proteome composition and nonspecific intermolecular interactions in regulating macromolecule diffusion and organization. Despite this, the dependence of diffusion-interaction on physicochemical properties such as the degree of poly-dispersity and the balance between steric repulsion and nonspecific attraction among macromolecules was not systematically addressed. In this work, we study the problem of diffusion-interaction in the bacterial cytoplasm, combining theory and experimental data to build a minimal coarse-grained representation of the cytoplasm, which also includes, for the first time to our knowledge, the nucleoid. With stochastic molecular-dynamics simulations of a virtual cytoplasm we are able to track the single biomolecule motion, sizing from 3 to 80 nm, on submillisecond-long trajectories. We demonstrate that the size dependence of diffusion coefficients, anomalous exponents, and the effective viscosity experienced by biomolecules in the cytoplasm is fine-tuned by the intermolecular interactions. Accounting only for excluded volume in these potentials gives a weaker size-dependence than that expected from experimental data. On the contrary, adding nonspecific attraction in the range of 1–10 thermal energy units produces a stronger variation of the transport properties at growing biopolymer sizes. Normal and anomalous diffusive regimes emerge straightforwardly from the combination of high macromolecular concentration, poly-dispersity, stochasticity, and weak nonspecific interactions. As a result, small biopolymers experience a viscous cytoplasm, while the motion of big ones is jammed because the entanglements produced by the network of interactions and the entropic effects caused by poly-dispersity are stronger.

Solvation free energies in [bmim]-based ionic liquids: Anion effect toward solvation of amino acid side chain analogues

Stochastic molecular dynamics simulations were performed to investigate the solvation free energy of 15 neutral amino acid side chain analogues in aqueous and five, 1-butyl-3-methylimidazolium ([BMIM])-based ionic liquids. The results in aqueous were found highly correlated with previous experimental and simulation data. Meanwhile, [BMIM]-based RTILs showed better solvation thermodynamics than water to an extent that they were capable of solvating molecules immiscible in water. Non-polar analogues showed stronger solvation in hydrophobic RTIL anions such as [PF6]− and [Tf2N]− while polar analogues showed stronger solvation in the more hydrophilic RTIL anions such as [Cl]−, [TfO]− and [BF4]−.

Structure, entanglements and dynamics of polymer nanocomposites containing spherical nanoparticles

We investigate the effect of nanoparticles on polymer structure, nanoparticle dynamics and topological constraints (entanglements) in polymer melts for nanoparticle loading above percolation threshold as high as 40.9% using stochastic molecular dynamics (MD) simulations. An increase in the number of entanglements (decrease of Ne with 40.9% volume fraction of nanoparticles dispersed in the polymer matrix) in the nanocomposites is observed as evidenced by larger contour lengths of the primitive paths. Attraction between polymers and nanoparticles affects the entanglements in the nanocomposites and alters the primitive path. The diffusivity of small sized nanoparticles deviates significantly from the Stokes- Einstein relation.

Structure, dynamics and primitive path network of polymer nanocomposites containing spherical nanoparticles

ABSTRACTWe investigate the effect of nanoparticles on polymer structure, polymer dimensions and topological constraints (entanglements) in polymer melts for nanoparticle loading above percolation threshold as high as 40.9% using stochastic molecular dynamics (MD) simulations. We show unambiguously that short polymer chains are not disturbed by the presence of repulsive nanoparticles. In contrast entangled polymer chains can be perturbed by the presence of attractive nanoparticles when the polymer radius of gyration is larger than the nanoparticle radius. They can expand under the presence of attractive nanoparticles even at low nanoparticle loadings of very small nanoparticle size. We observe an increase in the number of entanglements (decrease of Ne with 40.9% volume fraction of nanoparticles dispersed in the polymer matrix) in the nanocomposites as evidenced by larger contour lengths of the primitive paths. Attraction between polymers and nanoparticles affects the entanglements in the nanocomposites and alters the primitive path.

Altering Residues N125 and D149 Impacts Sugar Effector Binding and Allosteric Parameters in Escherichia coli Lactose Repressor

Lactose repressor protein (LacI), a negative transcriptional regulator in Escherichia coli, relies on an allosteric conformational change for its function. The LacI effector isopropyl-β,D-thiogalactoside (IPTG) promotes this allosteric response and engages the side chains of residues N125 and D149 based on the crystallographic structure of LacI·IPTG. Targeted molecular dynamics (TMD) simulations have indicated involvement of these side chains during the protein structural changes in response to inducer binding. To examine this region further, we applied stochastic boundary molecular dynamics (SBMD) simulation and identified a transient interaction between residues N125 and D149. On the basis of these data, we introduced substitutions for either/both residues and analyzed their impact on protein function. The substitutions utilized were alanine to preclude hydrogen bonding or cysteine to allow disulfide bond formation, which was not observed for N125C/D149C. Minimal impacts were observed on operator affinity for all substitutions, but D149C, N125A/D149A, and N125C/D149C bound to IPTG with 5-8-fold lower affinity than wild-type LacI, and exhibited decreased allosteric amplitude (K(RI/O)/K(R/O)). Of interest, the double mutants did not exhibit an allosteric response to an alternate inducer, 2-phenylethyl-β,D-galactoside (PhEG), despite demonstration of PhEG binding. Further, the presence of the anti-inducer, o-nitrophenyl-β,D-fucoside (ONPF), enhanced operator affinity for wild-type LacI and all other mutant proteins examined, but behaved as an inducer for N125A/D149A, decreasing operator binding affinity. These results confirm the role of residues 125 and 149 in ligand binding and allosteric response and illustrate how readily the function of a regulatory protein can be altered.

Effect of osteogenesis imperfecta mutations on free energy of collagen model peptides: A molecular dynamics simulation

We have carried out stochastic boundary molecular dynamics simulations to estimate free energy changes for substitutions of Gly with Val, Arg and Trp residues in a collagen-like peptide. The relative free energy change differences of mutants containing a Val, an Arg and a Trp relative to the wild type are 5.7, 8.1 and 9.5 kcal/mol, respectively. The corresponding free energy change differences of mutants containing two mutated residues are on average 7.6, 10.5 and 14.7 kcal/mol, respectively. We show that the free energy change differences are correlated with the severity of OI from statistical analysis and mechanical properties of the individual tropocollagen molecules. This simulation result indicates an atomistic-level mechanistic understanding of the effect of OI mutations in terms of stability of the mutants relative to the wild type, which could eventually provide a new strategy for diagnosis and treatment of the disease.

Anomalous chain diffusion in polymer nanocomposites for varying polymer-filler interaction strengths

Anomalous diffusion of polymer chains in a polymer nanocomposite melt is investigated for different polymer-nanoparticle interaction strengths using stochastic molecular dynamics simulations. For spherical nanoparticles dispersed in a polymer matrix the results indicate that the chain motion exhibits three distinct regions of diffusion, the Rouse-like motion, an intermediate subdiffusive regime followed by a normal Fickian diffusion. The motion of the chain end monomers shows a scaling that can be attributed to the formation of strong "networklike" structures, which have been seen in a variety of polymer nanocomposite systems. Irrespective of the polymer-particle interaction strengths, these three regimes seem to be present with small deviations. Further investigation on dynamic structure factor shows that the deviations simply exist due to the presence of strong enthalpic interactions between the monomers with the nanoparticles, albeit preserving the anomaly in the chain diffusion. The time-temperature superposition principle is also tested for this system and shows a striking resemblance with systems near glass transition and biological systems with molecular crowding. The universality class of the problem can be enormously important in understanding materials with strong affinity to form either a glass, a gel or networklike structures.

Modeling Entangled Dynamics: Comparison between Stochastic Single-Chain and Multichain Models

To test the effectiveness of stochastic single-chain models in describing the dynamics of entangled polymers, we systematically compare one such model—the slip−spring model—to a multichain model solved using stochastic molecular dynamics (MD) simulations (the Kremer−Grest model). The comparison involves investigating if the single-chain model can adequately describe both a microscopic dynamical and a macroscopic rheological quantity for a range of chain lengths. Choosing a particular chain length in the slip−spring model, the parameter values that best reproduce the mean-square displacement of a group of monomers is determined by fitting to MD data. Using the same set of parameters we then test if the predictions of the mean-square displacements for other chain lengths agree with the MD calculations. We followed this by a comparison of the time dependent stress relaxation moduli obtained from the two models for a range of chain lengths. After identifying a limitation of the original slip−spring model in describing the static structure of the polymer chain as seen in MD, we remedy this by introducing a pairwise repulsive potential between the monomers in the chains. Poor agreement of the mean-square monomer displacements at short times can be rectified by the use of generalized Langevin equations for the dynamics and resulted in significantly improved agreement.

Effect of polymer-filler interaction strengths on the thermodynamic and dynamic properties of polymer nanocomposites

The structural and dynamical properties of polymer nanocomposites are investigated using stochastic molecular dynamics simulations. For spherical nanoparticles dispersed in a polymer matrix, the results indicate that the polymer-nanoparticle interaction strength and the overall system temperature are primarily responsible for the type of dispersed state (clustering and homogeneous dispersion) achieved. A systematic study probing temperature, polymerization, and polymer-nanoparticle and nanoparticle-nanoparticle interaction strengths has been performed. In this paper, however, we focus the discussion on the results for varying polymer-nanoparticle interaction strengths at different temperatures. By examining the structure and dynamics, we show that there are two kinds of "clustering transitions:" one due to thermodynamic and another due to the dynamical response of the system. From these results, a representative phase diagram is developed that captures the entire simulated space and allows the easy identification of the highly dispersed and the clustered states.

FORMATION AND GROWTH OF CLUSTERS IN COLLOIDAL SUSPENSIONS

Depending on the p H -value and salt concentration of Al 2 O 3 suspensions different microstructures can form. Especially the clustered one is of major interest for industrial purposes as found in the production of ceramics. In this paper we investigate the clustered microstructure by means of a coupled Stochastic Rotation Dynamics (SRD) and Molecular Dynamics (MD) simulation. In order to gain statistics within a system containing numerous clusters, large simulation volumes are needed. We present our parallel implementation of the simulation algorithm as well as a newly developed cluster detection and tracking algorithm. We then show first results of measured growth rates and cluster size distributions to validate the applicability of our method.

Simulation study of cyclic-tethered nanocube self-assemblies: effect of tethered nanocubearchitectures

Self-assembly of functionalized nano building blocks (NBBs) is a promising avenue for‘bottom-up’ nanomaterials design. Experimental studies on functionalized polyhedraloligomeric silsesquioxane (POSS) nanocubes have revealed a wide variety of nanostructuresfrom their assemblies. Our previous simulation studies have reproduced some of thesenanostructures and predicted unusual phase behaviours imparted by the unique geometryof the nanocubes and their close packing patterns. Recent experiments further inspire us toexplore the effects of tether topologies on functionalized nanocube self-assemblies. We use asimplified model and perform stochastic molecular dynamics simulations to map themorphological phase diagrams of cyclic tethered nanocubes with varying tether topology,tether number, and tether placement. Our results illustrate that the steric influence ofthe tethers can be manipulated to confer precise control over the self-assemblednanostructures and the phase behaviour. The novel controlling factors investigated in ourstudy suggest new opportunities in controlling functionalized NBB self-assemblies.

Corrigendum to “Ion transfer across liquid–liquid interfaces from transition-state theory and stochastic molecular dynamics simulations” [JEC 590(2) (2006) 138–144

We investigate the kinetics and dynamics of ion transfer across liquid–liquid interfaces. We calculate the potential 0022-0728/$ see front matter 2006 Elsevier B.V. All rights reserved. doi:10.1016/j.jelechem.2006.10.001 DOI of original article: 10.1016/j.jelechem.2006.02.032 * Corresponding author. E-mail address: wolfgang.schmickler@uni-ulm.de (W. Schmickler). of mean force (pmf) of ion transfer from Monte Carlo simulations of a lattice–gas model, assuming independent chemical and electrostatic contributions. The shape of the pmf justifies considering the transfer as activated. The kinetics are obtained from transition-state theory and independently from stochastic molecular dynamics simulations. Both methods yield consistent results, with straight Tafel plots and friction effects in line with Kramers’ theory, but stronger than for a diffusing particle. A higher friction makes barrier recrossing more likely.

Ion transfer across liquid∣liquid interfaces from transition-state theory and stochastic molecular dynamics simulations

Abstract We investigate the kinetics and dynamics of ion transfer across liquid∣liquid interfaces. We calculate the potential of mean force (pmf) of ion transfer from Monte Carlo simulations of a lattice–gas model, assuming independent chemical and electrostatic contributions. The shape of the pmf justifies considering the transfer as activated. The kinetics are obtained from transition-state theory and independently from stochastic molecular dynamics simulations. Both methods yield consistent results, with straight Tafel plots and friction effects in line with Kramers’ theory, but stronger than for a diffusing particle. A higher friction makes barrier recrossing more likely.

Brownian dynamics of mixed surfactant micelles

We investigate micelle formation in a system containing two or more different amphiphiles with different geometries using a stochastic molecular-dynamics (MD) simulation method. For a binary system containing two amphiphiles, we calculate the critical micelle concentration (CMC) and cluster distribution for the mixture at several mole fractions and compare the simulation results with those predicted by analytic theories in the dilute limit and with experiments. We find that the CMC obtained from molecular mean-field theory agrees well with our simulation results. Motivated by the industrial use of mixed surfactant systems, we then extend our studies to a system containing six different chain lengths drawn from a Poisson distribution. We find that unlike a binary mixture of amphiphiles, the different species cancel the effects of each other so that the cluster distribution for the mixture has a shape of a system consisted entirely of amphiphiles of length equal to the mean chain length of the Poisson distribution.