[show abstract][hide abstract] ABSTRACT: We review pro and contra of the hypothesis that generic polymer properties of topological constraints are behind many aspects of chromatin folding in eukaryotic cells. For that purpose, we review, first, recent theoretical and computational findings in polymer physics related to concentrated, topologically simple (unknotted and unlinked) chains or a system of chains. Second, we review recent experimental discoveries related to genome folding. Understanding in these fields is far from complete, but we show how looking at them in parallel sheds new light on both.
Reports on Progress in Physics 01/2014; 77(2):022601. · 13.23 Impact Factor
[show abstract][hide abstract] ABSTRACT: For the example of C60 solutes in toluene, we present the implementation of the adaptive resolutions scheme (AdResS) for molecular simulations into GROMACS. In AdResS a local, typically all-atom cavity is coupled to a surrounding of coarse-grained, simplified molecules. This methodology can not only be used to reduce the CPU time demand of atomistic simulations but also to systematically investigate the relative influence of different interactions on structure formation. For this, we vary the thickness of the all atom layer of toluene around the C60 and analyze the first toluene layers in comparison to a full bulk simulation.
Journal of Chemical Theory and Computation 12/2013; 8(2):398. · 5.39 Impact Factor
[show abstract][hide abstract] ABSTRACT: Conformational transitions of (bio)macromolecules in aqueous mixtures are intimately linked to local concentration fluctuations of different solvent components. Though computer simulations are ideally suited to investigate such phenomena, in conventional setups the excess of one cosolvent close to the solute leads to depletion elsewhere, requiring very large simulations domain to avoid system size effects. We, here, propose an approach to overcome this depletion effect, which combines the Adaptive Resolution Scheme (AdResS) with a Metropolis particle exchange criterion. In AdResS, a small all-atom region, containing the solute, is coupled to a coarse-grained reservoir, where the particle exchange is performed.
The particle exchange would be almost impossible had they been performed in an all-atom setup of
a dense molecular liquid. We apply this approach to the reentrant collapse and swelling transition of
poly(N-isopropylacrylamide) in aqueous methanol mixtures and demonstrate the role of the delicate interplay of the different intermolecular interactions.
[show abstract][hide abstract] ABSTRACT: Complex soft matter systems can be efficiently studied with the help of adaptive resolution simulation methods, concurrently employing two levels of resolution in different regions of the simulation domain. The nonmatching properties of high- and low-resolution models, however, lead to thermodynamic imbalances between the system's subdomains. Such inhomogeneities can be healed by appropriate compensation forces, whose calculation requires nontrivial iterative procedures. In this work we employ the recently developed Hamiltonian adaptive resolution simulation method to perform Monte Carlo simulations of a binary mixture, and propose an efficient scheme, based on Kirkwood thermodynamic integration, to regulate the thermodynamic balance of multicomponent systems.
[show abstract][hide abstract] ABSTRACT: We investigate translocation mechanisms in smectic A liquid crystals (LCs) by a realistic, coarse-grained model of a LC compound comprising a stiff azobenzene core with flexible tails. We observe that the molecules can permeate from one smectic layer to the next via two different mechanisms, with and without significant reorientation, the former being facilitated through transverse interlayer intermediates. This is possible due to the intrinsic flexibility of the molecules. The two processes lead to characteristic signatures in the Van Hove self-correlation function, which can also be observed experimentally.
Physical Review E 07/2013; 88(1-1):010502. · 2.31 Impact Factor
[show abstract][hide abstract] ABSTRACT: Binary blends of polystyrene with oligostyrene are perfectly miscible (χ=0) yet dynamically heterogeneous. This is evidenced by independent probing of the dipole relaxation perpendicular to the backbone by dielectric spectroscopy and molecular dynamics. The self-concentration model with a single intramolecular length scale qualitatively describes the slower segmental dynamics. A quantitative comparison based on MD, however, requires a composition-dependent length scale. The pertinent dynamic length scale that best describes the slow segmental dynamics in miscible blends relates to both intra- and intermolecular contributions.
[show abstract][hide abstract] ABSTRACT: Adaptive resolution schemes allow the simulation of a molecular fluid
treating simultaneously different subregions of the system at different levels
of resolution. In this work we present a new scheme formulated in terms of a
global Hamiltonian. Within this approach equilibrium states corresponding to
well defined statistical ensembles can be generated making use of all standard
Molecular Dynamics or Monte Carlo methods. Models at different resolutions can
thus be coupled, and thermodynamic equilibrium can be modulated keeping each
region at desired pressure or density without disrupting the Hamiltonian
[show abstract][hide abstract] ABSTRACT: Coupling different level of resolutions within a unified molecular dynamics scheme seeks to
attain large time and length scale while retaining the full chemical detail only in the region of
interest. One such multiscale technique is the adaptive resolution molecular dynamic scheme
(AdResS). In AdResS, a high resolution all-atom region is coupled to a coarse-grained particle
reservoir. Implementing the AdResS scheme, for the (bio)macromolecular simulations, is of
particular importance, where the full chemical details are only important within a few nanometers
from the solvated protein. The remaining solvent molecules, that are present to maintain
equilibrium with the bulk solution, can be represented by single site coarse-grained beads. The
coupling leads to correct concentration fluctuations within the small all-atom region, making
the all-atom region an “effective” open boundary system. We treat this small all-atom region
within the framework of fluctuation theory of Kirkwood and Buff, derived for open systems.
We will present examples where this open boundary approach is successfully used to calculate
solvation free energies of aqueous mixtures.
[show abstract][hide abstract] ABSTRACT: To study the conformational properties of unknotted and nonconcatenated ring polymers in the melt, we present a detailed qualitative and quantitative comparison of simulation data obtained by molecular dynamics simulation using an off-lattice bead-spring model and by Monte Carlo simulation using a lattice model. We observe excellent, and sometimes even unexpectedly good, agreement between the off-lattice and lattice results for many quantities measured including the gyration radii of the ring polymers, gyration radii of their subchains, contact probabilities, surface characteristics, number of contacts between subchains, and the static structure factors of the rings and their subchains. These results are, in part, put in contrast to Moore curves, and the open, linear polymer counterparts. While our analysis is extensive, our understanding of the ring melt conformations is still rather preliminary.
Journal of Physics A Mathematical and Theoretical 01/2013; 46(6):065002. · 1.77 Impact Factor
[show abstract][hide abstract] ABSTRACT: We establish a link between the microscopic ordering and the charge-transport parameters for a highly crystalline polymeric organic semiconductor, poly(2,5-bis(3-tetradecylthiophen-2-yl)thieno[3,2-b]thiophene) (PBTTT). We find that the nematic and dynamic order parameters of the conjugated backbones, as well as their separation, evolve linearly with temperature, while the side-chain dynamic order parameter and backbone paracrystallinity change abruptly upon the (also experimentally observed) melting of the side chains around 400 K. The distribution of site energies follows the behavior of the backbone paracrystallinity and can be treated as static on the time scale of a single-charge transfer reaction. On the contrary, the electronic couplings between adjacent backbones are insensitive to side-chain melting and vary on a much faster time scale. The hole mobility, calculated after time-averaging of the electronic couplings, reproduces well the value measured in a short-channel thin-film transistor. The results underline that to secure efficient charge transport in lamellar arrangements of conjugated polymers: (i) the electronic couplings should present high average values and fast dynamics, and (ii) the energetic disorder (paracrystallinity) should be small.
The Journal of Physical Chemistry C 01/2013; 117(4):1633-1640. · 4.81 Impact Factor
[show abstract][hide abstract] ABSTRACT: The redesigned Extensible Simulation Package for Research on Soft matter systems (ESPResSo++) is a free, open-source, parallelized, object-oriented simulation package designed to perform many-particle simulations, principally molecular dynamics and Monte Carlo, of condensed soft matter systems. In addition to the standard simulation methods found in well-established packages, ESPResSo++ provides the ability to perform Adaptive Resolution Scheme (AdResS) simulations which are multiscale simulations of molecular systems where the level of resolution of each molecule can change on-the-fly. With the main design objective being extensibility, the software features a highly modular C++ kernel that is coupled to a Python user interface. This makes it easy to add new algorithms, setup a simulation, perform online analysis, use complex workflows and steer a simulation. The extreme flexibility of the software allows for the study of a wide range of systems. The modular structure enables scientists to use ESPResSo++ as a research platform for their own methodological developments, which at the same time allows the software to grow and acquire the most modern methods. ESPResSo++ is targeted for a broad range of architectures and is licensed under the GNU General Public License.
[show abstract][hide abstract] ABSTRACT: We present an adaptive resolution simulation of aqueous salt (NaCl) solutions at ambient conditions using the adaptive resolution scheme. Our multiscale approach concurrently couples the atomistic and coarse-grained models of the aqueous NaCl, where water molecules and ions change their resolution while moving from one resolution domain to the other. We employ standard extended simple point charge (SPC/E) and simple point charge (SPC) water models in combination with AMBER and GROMOS force fields for ion interactions in the atomistic domain. Electrostatics in our model are described by the generalized reaction field method. The effective interactions for water–water and water–ion interactions in the coarse-grained model are derived using structure-based coarse-graining approach while the Coulomb interactions between ions are appropriately screened. To ensure an even distribution of water molecules and ions across the simulation box we employ thermodynamic forces. We demonstrate that the equilibrium structural, e.g. radial distribution functions and density distributions of all the species, and dynamical properties are correctly reproduced by our adaptive resolution method. Our multiscale approach, which is general and can be used for any classical non-polarizable force-field and/or types of ions, will significantly speed up biomolecular simulation involving aqueous salt.
New Journal of Physics 01/2013; 15:105007. · 4.06 Impact Factor
[show abstract][hide abstract] ABSTRACT: Coupling different levels of resolutions within a unified molecular dynamics scheme seeks to
attain large time and length scale while keeping the full chemical detail in the region of high
resolution. One such multi-scale technique is the adaptive resolution molecular dynamic scheme
(AdResS). In AdResS, a high resolution all-atom region is coupled with a much larger coarse-grained
particle reservoir, where particle exchange is allowed, on-the-fly, in thermodynamic
equilibrium. Implementing this approach is of particular advantage when simulating solvation
thermodynamics of biologically relevant aqueous mixtures. For example, coupling of high
resolution all-atom system to a much larger osmotic coarse-grained region ensures a overall
solvent equilibrium, which is extremely relevant in studying liquid mixtures. Therefore, the
all-atom region can be considered as an “effective” open boundary. We treat this small all-atom
region within the framework of fluctuation theory of Kirkwood and Buff. We will present
examples where this open boundary approach can be efficiently implemented to study the aqueous
[show abstract][hide abstract] ABSTRACT: Structure-based coarse-graining relies on matching the pair correlation functions of a reference (atomistic) and a coarse-grained system. As such, it is designed for systems with uniform density distributions. Here, we demonstrate how it can be generalized for inhomogeneous systems by coarse-graining slabs of liquid water and methanol in vacuum, as well as a single benzene molecule at the water-vacuum interface. Our conclusion is that coarse-graining performed in inhomogeneous systems improves thermodynamic properties and the structure of interfaces without significant alterations to the local structure of the bulk liquid.
The Journal of Chemical Physics 08/2012; 137(6):064102. · 3.16 Impact Factor
[show abstract][hide abstract] ABSTRACT: We develop a hybrid Monte Carlo approach for modelling nematic liquid crystals of homopolymer melts. The polymer architecture is described with a discrete worm-like chain model. A quadratic density functional accounts for the limited compressibility of the liquid, while an additional quadratic functional of the local orientation tensor of the segments captures the nematic ordering. The approach can efficiently address large systems parametrized according to volumetric and conformational properties, representative of real polymeric materials. The results of the simulations regarding the influence of the molecular weight on the isotropic-nematic transition are compared to predictions from a Landau-de Gennes free energy expansion. The formation of the nematic phase is addressed within Rouse-like dynamics, realized using the current model.
[show abstract][hide abstract] ABSTRACT: Solvation free energies of peptides in water decrease with increasing urea concentration and therefore lead to increased solubility. In this work, we study the solvation thermodynamics of a tri-glycine in aqueous urea solution at room temperature T=300K. We perform our analysis within the framework of the Kirkwood-Buff theory of liquid mixtures, developed for open systems. For this purpose, we use a recently proposed approach to study liquid mixtures in an ``effective" open boundary simulation scheme (AdResS). We couple a small open boundary all-atom (explicit) region to a much larger coarse-grained particle reservoir. This coupling allows the free exchange of particles in thermodynamic equilibrium. Our approach preserves correct particle fluctuations that are important for studying the concentration driven conformational transition of (bio)molecules.
Journal of Chemical Theory and Computation 07/2012; 8:3536. · 5.39 Impact Factor
[show abstract][hide abstract] ABSTRACT: For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open regions of different resolution or representation. We generalize the adaptive resolution idea and suggest an interpretation in terms of an effective generalized grand canonical approach. The method is applied to liquid water at ambient conditions.
[show abstract][hide abstract] ABSTRACT: A bottom-up coarse-graining procedure for peptides in aqueous solution is presented, where the interactions in the coarse-grained (CG) model are determined such that the CG peptide samples conformations according to a high-resolution (atomistic) model. It is shown that important aspects of conformational sampling, such as correlated degrees of freedom (DOF) which play an important role in secondary structure formation, can be reproduced in the CG description. In some cases, microscopic structural/conformational details are lost in the coarse-graining process. We show that these "lost" properties can be recovered in a backmapping procedure which reintroduces atomistic DOF into CG structures - as long as the overall conformational sampling of the molecule is correctly represented in the CG level of resolution. Thus, it is possible to link an existing all-atom model of a biomolecular system with a CG description such that after inverse mapping one can recover structures at high resolution with the correctly sampled (according to the atomistic model) conformational properties.
Journal of Computational Chemistry 04/2012; 33(9):937-49. · 3.84 Impact Factor
[show abstract][hide abstract] ABSTRACT: We present a systematic derivation of a coarse grained (CG) model for molecular dynamics (MD) simulations of a liquid crystalline (LC) compound containing an azobenzene mesogen. The model aims at a later use in a multiscale modeling approach to study liquid crystalline phase transitions that are (photo)induced by the trans/cis photoisomerization of the mesogen. One of the major challenges in the coarse graining process is the development of models that are for a given chemical system structurally consistent with for example an all-atom reference model and reproduce relevant thermodynamic properties such as the LC phase behavior around the state point of interest. The reduction of number of degrees of freedom makes the resulting coarse models by construction state point dependent; that is, they cannot easily be transferred to a range of temperatures, densities, system compositions, etc. These are significant challenges, in particular if one wants to study LC phase transitions (thermally or photoinduced). In the present paper we show how one can systematically derive a CG model for a LC molecule that is highly consistent with an atomistic description by choosing an appropriate state point for the reference simulation. The reference state point is the supercooled liquid just below the smectic-isotropic phase transition which is characterized by a high degree of local nematic order while being overall isotropic. With the resulting CG model it is possible to switch between the atomistic and the CG levels (and vice versa) in a seamless manner maintaining values of all the relevant order parameters which describe the smectic A (smA) state. This model will allow us in the future to link large length scale and long time scale CG simulations of the LC state with chemically accurate QM/MM simulations of the photoisomerization process.
The Journal of Physical Chemistry B 04/2012; 116(29):8474-84. · 3.61 Impact Factor