[Show abstract][Hide abstract] ABSTRACT: We show here that molecular resolution is inherently hybrid in terms of relative separation. While nearest neighbors are characterized by a fine-grained (geometrically detailed) model, other neighbors are characterized by a coarse-grained (isotropically simplified) model. We notably present an analytical expression for relating the two models via energy conservation. This hybrid framework is correspondingly capable of retrieving the structural and thermal behavior of various multi-component and multi-phase fluids across state space.
The Journal of Chemical Physics 12/2015; 143(24):243107. DOI:10.1063/1.4929834 · 2.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: It is well known that poly(N-isopropylacrylamide) (PNIPAm) exhibits an interesting, yet puzzling, phenomenon of co-non-solvency. Co-non-solvency occurs when two competing good solvents for PNIPAm, such as water and alcohol, are mixed together. As a result, the same PNIPAm collapses within intermediate mixing ratios. This complex conformational transition is driven by preferential binding of methanol with PNIPAm. Interestingly, co-non-solvency can be destroyed when applying high hydrostatic pressures. In this work, using a large scale molecular dynamics simulation employing high pressures, we propose a microscopic picture behind the suppression of the co-non-solvency phenomenon. Based on thermodynamic and structural analysis, our results suggest that the preferential binding of methanol with PNIPAm gets partially lost at high pressures, making the background fluid reasonably homogeneous for the polymer. This is consistent with the hypothesis that the co-non-solvency phenomenon is driven by preferential binding and is not based on depletion effects.
[Show abstract][Hide abstract] ABSTRACT: The correct interplay of interactions between protein, pigment and lipid molecules is highly relevant for our understanding of the association behavior of the light harvesting complex (LHCII) of green plants. To cover the relevant time and length scales in this multicomponent system, a multi-scale simulation ansatz is employed that subsequently uses a classical all atomistic (AA) model to derive a suitable coarse grained (CG) model which can be backmapped into the AA resolutions, aiming for a seamless conversion between two scales. Such an approach requires a faithful description of not only the protein and lipid components, but also the interaction functions for the indispensable pigment molecules, chlorophyll b and chlorophyll a (referred to as chl b/chl a). In this paper we develop a CG model for chl b and chl a in a dipalmitoylphosphatidyl choline (DPPC) bilayer system. The structural properties and the distribution behavior of chl within the lipid bilayer in the CG simulations are consistent with those of atomistic reference simulations. The non-bonded potentials are parameterized such that they fit to the thermodynamics based MARTINI force-field for the lipid bilayer and the protein. The CG simulation shows chl aggregation in the lipid bilayer which is supported by fluorescence quenching experiments. It is shown that the derived chl model is well suited for CG simulations of stable, structurally-consistent, trimeric LHCII and can in the future be used to study their large scale aggregation behavior.
[Show abstract][Hide abstract] ABSTRACT: Mesoscale behavior of polymers is frequently described by universal laws. This physical property motivates us to propose a new modeling concept, grouping polymers into classes with a common long-wavelength representation. In the same class, samples of different materials can be generated from this representation, encoded in a single library system. We focus on homopolymer melts, grouped according to the invariant degree of polymerization. They are described with a bead-spring model, varying chain stiffness and density to mimic chemical diversity. In a renormalization group-like fashion, library samples provide a universal blob-based description, hierarchically backmapped to create configurations of other class-members. Thus, large systems with experimentally relevant invariant degree of polymerizations (so far accessible only on very coarse-grained level) can be microscopically described. Equilibration is verified comparing conformations and melt structure with smaller scale conventional simulations.
The Journal of Chemical Physics 06/2015; 142(22):221102. DOI:10.1063/1.4922538 · 2.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Topological constraints due to chain connectivity and uncrossability greatly impact the long time dynamics and rheology of high molecular weight polymer melts. Computer simulations to study properties of such melts are very advantageous, since perfect control of molecular conformation and melt morphology is available. We present a methodology to prepare well-equilibrated polymer melts which only requires local relaxation. The approach efficiently leads to equilibrated ensembles of bead-spring polymer melts of 1 000 chains of up to 2 000 beads, which correspond to 24 (fully flexible) and 45 entanglement lengths (semi-flexible chains). Entanglements are identified by a primitive path analysis and a master curve of the entanglement lengths for different chain and persistence lengths is presented.
Macromolecular Theory and Simulations 06/2015; 24(5). DOI:10.1002/mats.201500013 · 1.67 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: A fully atomistic modelling of many biophysical and biochemical processes at biologically relevant length- and time scales is beyond our reach with current computational resources, and one approach to overcome this difficulty is the use of multiscale simulation techniques. In such simulations, when system properties necessitate a boundary between resolutions that falls within the solvent region, one can use an approach such as the Adaptive Resolution Scheme (AdResS), in which solvent particles change their resolution on the fly during the simulation. Here, we apply the existing AdResS methodology to biomolecular systems, simulating a fully atomistic protein with an atomistic hydration shell, solvated in a coarse-grained particle reservoir and heat bath. Using as a test case an aqueous solution of the regulatory protein ubiquitin, we first confirm the validity of the AdResS approach for such systems, via an examination of protein and solvent
structural and dynamical properties. We then demonstrate how, in addition to providing a computational speedup, such a multiscale AdResS approach can yield otherwise inaccessible physical insights into biomolecular function. We use our methodology to show that protein
structure and dynamics can still be correctly modelled using only a few shells of atomistic water molecules. We also discuss aspects of the AdResS methodology peculiar to biomolecular simulations.
The Journal of Chemical Physics 05/2015; 142(19):195101. DOI:10.1063/1.4921347 · 2.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In computer simulations, quantum delocalization of atomic nuclei can be
modeled making use of the Path Integral (PI) formulation of quantum statistical
mechanics. This approach, however, comes with a large computational cost. By
restricting the PI modeling to a small region of space, this cost can be
significantly reduced. In the present work we derive a Hamiltonian formulation
for a bottom-up, theoretically solid simulation protocol that allows molecules
to change their resolution from quantum-mechanical to classical and vice versa
on the fly, while freely diffusing across the system. This approach renders
possible simulations of quantum systems at constant chemical potential. The
validity of the proposed scheme is demonstrated by means of simulations of low
temperature parahydrogen. Potential future applications include simulations of
biomolecules, membranes, and interfaces.
[Show abstract][Hide abstract] ABSTRACT: Crystallisation of liquid solutions is of uttermost importance in a wide variety of processes in materials, atmospheric and food science. Depending on the type and concentration of solutes the freezing point shifts, thus allowing control on the thermodynamics of complex fluids. Here we investigate the basic principles of solute-induced freezing point depression by computing the melting temperature of a Lennard-Jones fluid with low concentrations of solutes, by means of equilibrium molecular dynamics simulations. The effect of solvophilic and weakly solvophobic solutes at low concentrations is analysed, scanning systematically the size and the concentration. We identify the range of parameters that produce deviations from the linear dependence of the freezing point on the molal concentration of solutes, expected for ideal solutions. Our simulations allow us also to link the shifts in coexistence temperature to the microscopic structure of the solutions.
[Show abstract][Hide abstract] ABSTRACT: Smart polymers are a modern class of polymeric materials that often exhibit
unpredictable behavior in mixtures of solvents. One such phenomenon is
co-non-solvency. Co-non-solvency occurs when two (perfectly) miscible and
competing good solvents, for a given polymer, are mixed together. As a result,
the same polymer collapses into a compact globule within intermediate mixing
ratios. More interestingly, polymer collapses when the solvent quality remains
good and even gets increasingly better by the addition of the better cosolvent.
This is a puzzling phenomenon that is driven by strong local concentration
fluctuations. Because of the discrete particle based nature of the
interactions, Flory-Huggins type mean field arguments become unsuitable. In
this work, we extend the analysis of the co-non-solvency effect presented
earlier [Nature Communications 5, 4882 (2014)]. We explain why co-non-solvency
is a generic phenomenon that can be understood by the thermodynamic treatment
of the competitive displacement of (co)solvent components. This competition can
result in a polymer collapse upon improvement of the solvent quality. Specific
chemical details are not required to understand these complex conformational
transitions. Therefore, a broad range of polymers are expected to exhibit
similar reentrant coil-globule-coil transitions in competing good solvents.
The Journal of Chemical Physics 02/2015; 142(11). DOI:10.1063/1.4914870 · 2.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: In adaptive resolution simulations, molecular fluids are modeled employing
different levels of resolution in different subregions of the system. When
traveling from one region to the other, particles change their resolution on
the fly. One of the main advantages of such approaches is the computational
efficiency gained in the coarse-grained region. In this respect the best
coarse-grained system to employ in the low resolution region would be the ideal
gas, making intermolecular force calculations in the coarse-grained subdomain
redundant. In this case, however, a smooth coupling is challenging due to the
high energetic imbalance between typical liquids and a system of
non-interacting particles. In the present work, we investigate this approach,
using as a test case the most biologically relevant fluid, water. We
demonstrate that a successful coupling of water to the ideal gas can be
achieved with current adaptive resolution methods, and discuss the issues that
remain to be addressed.
The European Physical Journal Special Topics 12/2014; 224(12). DOI:10.1140/epjst/e2015-02533-5 · 1.40 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: This chapter summarizes several approaches combining theory, simulation and
experiment that aim for a better understanding of phenomena in lipid bilayers
and membrane protein systems, covering topics such as lipid rafts, membrane
mediated interactions, attraction between transmembrane proteins, and
aggregation in biomembranes leading to large superstructures such as the light
harvesting complex of green plants. After a general overview of theoretical
considerations and continuum theory of lipid membranes we introduce different
options for simulations of biomembrane systems, addressing questions such as:
What can be learned from generic models? When is it expedient to go beyond
them? And what are the merits and challenges for systematic coarse graining and
quasi-atomistic coarse grained models that ensure a certain chemical
[Show abstract][Hide abstract] ABSTRACT: Atomistic molecular dynamics simulations of a chemically realistic model of atactic short-chain polystyrene between gold surfaces (111) and positron annihilation lifetime spectroscopy experiments on similar polystyrene thin films on gold were performed. Results from both approaches show that the free volume voids in the film have a slightly smaller average size than in bulk polystyrene. In agreement to that the existence of an interphase of higher density at the polymer–solid substrate interface is shown both by the simulation as well as in the experiment. The average shape of the voids is similar in the bulk and the film.
[Show abstract][Hide abstract] ABSTRACT: Adaptive resolution schemes enable molecular dynamics simulations of liquids and soft matter employing two different resolution levels concurrently in the same setup. These methods are based on a position-dependent interpolation of either forces or potential energy functions. While force-based methods generally lead to non-conservative forces, energy-based ones include undesired force terms proportional to the gradient of the interpolation function. In this work we establish a so far missing bridge between these formalisms making use of the generalized Langevin equation, thereby providing a unifying framework to traditionally juxtaposed approaches to adaptive simulations.
[Show abstract][Hide abstract] ABSTRACT: In the last few decades, computer simulations have become a fundamental tool in the field of soft matter science, allowing researchers to investigate the properties of a large variety of systems. Nonetheless, even the most powerful computational resources presently available are, in general, sufficient to simulate complex biomolecules only for a few nanoseconds. This limitation is often circumvented by using coarse-grained models, in which only a subset of the system's degrees of freedom is retained; for an effective and insightful use of these simplified models; however, an appropriate parametrization of the interactions is of fundamental importance. Additionally, in many cases the removal of fine-grained details in a specific, small region of the system would destroy relevant features; such cases can be treated using dual-resolution simulation methods, where a subregion of the system is described with high resolution, and a coarse-grained representation is employed in the rest of the simulation domain. In this review we discuss the basic notions of coarse-graining theory, presenting the most common methodologies employed to build low-resolution descriptions of a system and putting particular emphasis on their similarities and differences. The AdResS and H-AdResS adaptive resolution simulation schemes are reported as examples of dual-resolution approaches, especially focusing in particular on their theoretical background.
[Show abstract][Hide abstract] ABSTRACT: The Adaptive Resolution Scheme (AdResS) is a hybrid scheme that allows one to
treat a molecular system with different levels of resolution depending on the
location of the molecules. The construction of a Hamiltonian based on the this
idea (H-AdResS) allows one to formulate the usual tools of ensembles and
statistical mechanics. We present a number of exact and approximate results
that provide a statistical mechanics foundation for this simulation method. We
also present simulation results that illustrate the theory.
The Journal of Chemical Physics 07/2014; 142(6). DOI:10.1063/1.4907006 · 2.95 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Water and alcohol, such as methanol or ethanol, are miscible and, individually, good solvents for
several smart polymers, but this polymer precipitates in water-alcohol mixtures. The intriguing behavior of solvent mixtures that cannot dissolve a given polymer or a given protein, while the same macromolecule dissolves well in each of the cosolvents, is called cononsolvency. It is a widespread phenomenon, relevant for many formulation steps in the physicochemical and pharmaceutical industry, that is usually explained by invoking specific chemical details of the mixtures: as such it has so far eluded any generic explanation. Here, by using a combination of simulations and theory, we present a simple and universal treatment that requires only the preferential interaction of one of the cosolvents with the polymer. The results show striking quantitative agreement with experiments and chemically specific simulations, opening a new perspective towards an operational understanding of macromolecular solubility.