Search

Science is and always has been based on data, but the terms "data-centric" and the "4th paradigm of" materials research indicate a radical change in how information is retrieved, handled and research is performed. It signifies a transformative shift towards managing vast data collections, digital repositories, and innovative data analytics methods. The integration of Artificial Intelligence (AI) and its subset Machine Learning (ML), has become pivotal in addressing all these challenges. This Roadmap on Data-Centric Materials Science explores fundamental concepts and methodologies, illustrating diverse applications in electronic-structure theory, soft matter theory, microstructure research, and experimental techniques like photoemission, atom probe tomography, and electron microscopy. While the roadmap delves into specific areas within the broad interdisciplinary field of materials science, the provided examples elucidate key concepts applicable to a wider range of topics. The discussed instances offer insights into addressing the multifaceted challenges encountered in contemporary materials research., Comment: Review, outlook, roadmap, perspective

The glass transition temperature and its connection to statistical properties of confined and free-standing polymer films of varying thickness containing unentangled to highly entangled bead-spring chains are studied by molecular dynamics simulations. For confined films, perfect scaling of the thickness-dependent end-to-end distance and radius of gyrations normalized to their bulk values in the directions parallel and perpendicular to the surfaces is obtained. Particularly, the reduced end-to-end distance in the perpendicular direction is very well described by the extended Silberberg model. For bulk polymer melts, the relation between chain length and $T_g$ follows the Fox-Flory equation while $T_g$ for a given film thickness is almost independent of chain length. For films, $T_g$ decreases and is well described by Keddie's formula, where the reduction is more pronounced for free-standing films. For the present model, $T_g$ begins to deviate from bulk $T_g$ at the characteristic film thickness, where the average bond orientation becomes anisotropic and the entanglement density decreases., Comment: 6 pages, 4 figures, Supplementary Material (6 pages, 2 figures)

Urea denatures proteins due to its strong tendency to dehydrate the first solvation shell via urea-residue preferential binding. However, even after extensive experimental and computational investigations, the influence of urea on the stability of secondary structures remains elusive. For example, contrary to the common understanding, experimental studies have indicated that specific polypeptides, such as poly-alanine or alanine-rich systems, may even show an improved tendency to form secondary structures in aqueous urea. We investigate this seemingly counter-intuitive behaviour using over 15$\mu$s long all-atom simulations. These results show how a delicate balance between the localized dipole orientations and hydrogen bonding dictates polypeptide solvation in aqueous urea. Our work establishes a structure-property relationship that highlights the importance of microscopic dipole-dipole orientations/interactions for the operational understanding of macroscopic protein solvation.

Understanding the nature of glass transition, as well as precise estimation of the glass transition temperature for polymeric materials, remain open questions in both experimental and theoretical polymer sciences. We propose a data-driven approach, which utilizes the high-resolution details accessible through the molecular dynamics simulation and considers the structural information of individual chains. It clearly identifies the glass transition temperature of polymer melts of weakly semiflexible chains. By combining principal component analysis and clustering, we identify the glass transition temperature in the asymptotic limit even from relatively short-time trajectories, which just reach into the Rouse-like monomer displacement regime. We demonstrate that fluctuations captured by the principal component analysis reflect the change in a chain's behaviour: from conformational rearrangement above to small rearrangements below the glass transition temperature. Our approach is straightforward to apply, and should be applicable to other polymeric glass-forming liquids.

The prosperity and lifestyle of our society are very much governed by achievements in condensed matter physics, chemistry and materials science, because new products for sectors such as energy, the environment, health, mobility and information technology (IT) rely largely on improved or even new materials. Examples include solid-state lighting, touchscreens, batteries, implants, drug delivery and many more. The enormous amount of research data produced every day in these fields represents a gold mine of the twenty-first century. This gold mine is, however, of little value if these data are not comprehensively characterized and made available. How can we refine this feedstock; that is, turn data into knowledge and value? For this, a FAIR (findable, accessible, interoperable and reusable) data infrastructure is a must. Only then can data be readily shared and explored using data analytics and artificial intelligence (AI) methods. Making data 'findable and AI ready' (a forward-looking interpretation of the acronym) will change the way in which science is carried out today. In this Perspective, we discuss how we can prepare to make this happen for the field of materials science.

Motivated by chromosomes enclosed in nucleus and the recently discovered active topological glass, we study a spherically confined melt of long nonconcatenated active polymer rings. Without activity, the rings exhibit the same average large-scale conformational properties as chromatin fiber. Upon activating consecutive monomer segments on the rings, the system arrives at a glassy steady state due to activity-enhanced topological constraints. The latter generate coherent motions of the system, however the resulting large-scale structures are inconsistent with the fractal globule model. We observe microphase separation between active and passive segments without systematic trends in the positioning of active domains within the confining sphere. We find that tank-treading of active segments along the ring contour enhances active-passive phase separation in the state of active topological glass when both diffusional and conformational relaxation of the rings are significantly suppressed. Finally, although the present model of partly-active rings is not compatible with the large-scale chromatin organization, our results suggest that the activity-enhanced entanglements that result in facilitated intra- and inter-chromosomal contacts might be relevant for chromatin structure at smaller scales., Comment: 11 pages, 6 figures, 3 tables, supporting information

Room-temperature ionic liquids (RTILs) stand out among molecular liquids for their rich physicochemical characteristics, including structural and dynamic heterogeneity. The significance of electrostatic interactions in RTILs results in long characteristic length- and timescales, and has motivated the development of a number of coarse-grained (CG) simulation models. In this study, we aim to better understand the connection between certain CG parametrization strategies and the dynamical properties and transferability of the resulting models. We systematically compare five CG models: a model largely parametrized from experimental thermodynamic observables; a refinement of this model to increase its structural accuracy; and three models that reproduce a given set of structural distribution functions by construction, with varying intramolecular parametrizations and reference temperatures. All five CG models display limited structural transferability over temperature, and also result in various effective dynamical speedup factors, relative to a reference atomistic model. On the other hand, the structure-based CG models tend to result in more consistent cation-anion relative diffusion than the thermodynamic-based models, for a single thermodynamic state point. By linking short- and long-timescale dynamical behaviors, we demonstrate that the varying dynamical properties of the different coarse-grained models can be largely collapsed onto a single curve, which provides evidence for a route to constructing dynamically-consistent CG models of RTILs.

Responsiveness of polypeptides and polymers in aqueous solution plays an important role in biomedical applications and in designing advanced functional materials. Elastin-like polypeptides (ELPs) are a well-known class of synthetic intrinsically disordered proteins (IDPs), which exhibit a lower critical solution temperature (LCST) in pure water. The LCST transition can be further tuned by proline isomerization. Here, we study and compare the influence of cis/trans proline isomerization on the collapse of single ELPs in aqueous solution. Our results reveal that cis isomers play an important role in tuning the phase behavior of ELPs by hindering peptide-water hydrogen bonding while promoting intramolecular interactions., Comment: Under review of ACS Macro Letters

Equilibration of polymer melts containing highly entangled long polymer chains in confinement or with free surfaces is a challenge for computer simulations. We approach this problem by first studying polymer melts based on the soft-sphere coarse-grained model confined between two walls with periodic boundary conditions in two directions parallel to the walls. Then we apply backmapping to reinsert the microscopic details of the underlying bead-spring model. Tuning the strength of the wall potential, the monomer density of confined polymer melts in equilibrium is kept at the bulk density even near the walls. In a weak confining regime, we observe the same conformational properties of chains as in the bulk melt showing that our confined polymer melts have reached their equilibrated state. Our methodology provides an efficient way of equilibrating large polymer films with different thicknesses and is not confined to a specific underlying microscopic model. Switching off the wall potential in the direction perpendicular to the walls, enables to study free-standing highly entangled polymer films or polymer films with one supporting substrate., Comment: 26 pages, 11 figures

Polymorphism rationalizes how processing can control the final structure of a material. The rugged free-energy landscape and exceedingly slow kinetics in the solid state have so far hampered computational investigations. We report for the first time the free-energy landscape of a polymorphic crystalline polymer, syndiotactic polystyrene. Coarse-grained metadynamics simulations allow us to efficiently sample the landscape at large. The free-energy difference between the two main polymorphs, $\alpha$ and $\beta$, is further investigated by quantum-chemical calculations. The two methods are in line with experimental observations: they predict $\beta$ as the more stable polymorph at standard conditions. Critically, the free-energy landscape suggests how the $\alpha$ polymorph may lead to experimentally observed kinetic traps. The combination of multiscale modeling, enhanced sampling, and quantum-chemical calculations offers an appealing strategy to uncover complex free-energy landscapes with polymorphic behavior., Comment: 10 pages, 4 figures

The solvent quality determines the collapsed or the expanded state of a polymer. For example, a polymer dissolved in a poor solvent collapses, whereas in a good solvent it opens up. While this standard understanding is generally valid, there are examples when a polymer collapses even in a mixture of two good solvents. This phenomenon, commonly known as co-non-solvency, is usually associated with smart polymers. Moreover, recent experiments have shown that the elastin-like polypeptides (ELPs) show co-non-solvency behavior in aqueous-ethanol mixtures. In this study, we investigate the phase behavior of ELPs in aqueous binary mixtures using molecular dynamics simulations of all-atom and complementary explicit solvent generic models. The model is parameterized by mapping the solvation free energy obtained from the all-atom simulations onto the generic interaction parameters. For this purpose, we derive segment based generic parameters for four different peptides, namely proline (P), valine (V), glycine (G) and alanine (A). Here we compare the conformational behavior of two ELP sequences, namely VPGGG and VPGVG, in aqueous-ethanol and -urea mixtures. Consistent with recent experiments, we find that ELPs show co-non-solvency in aqueous-ethanol mixtures. Ethanol molecules have preferential binding with all ELP residues and thus driving the coil-to-globule transition. On the contrary, ELP conformations show weak variation in aqueous-urea mixtures. Our simulations suggest that the glycine residues dictate the overall behavior of ELPs in aqueous-urea, where urea molecules have a rather weak preferential binding with glycine, i.e., less than kT. While the validation of the latter findings will require more detailed experimental investigation, the results presented here may provide a new twist to the present understanding of cosolvent interactions with peptides and proteins., Comment: Accepted for publication in Macromolecules

A fully atomistic modelling of biological macromolecules at relevant length- and time-scales is often cumbersome or not even desirable, both in terms of computational effort required and it a posteriori analysis. This difficulty can be overcome with the use of multi-resolution models, in which different regions of the same system are concurrently described at different levels of detail. In enzymes, computationally expensive atomistic detail is crucial in the modelling of the active site in order to capture e.g. the chemically subtle process of ligand binding. In contrast, important yet more collective properties of the remainder of the protein can be reproduced with a coarser description. In the present work, we demonstrate the effectiveness of this approach through the calculation of the binding free energy of hen egg white lysozyme (HEWL) with the inhibitor di-N-acetylchitotriose. Particular attention is posed to the impact of the mapping, i.e. the selection of atomistic and coarse-grained residues, on the binding free energy. It is shown that, in spite of small variations of the binding free energy with respect to the active site resolution, the separate contributions coming from different energetic terms (such as electrostatic and van der Waals interactions) manifest a stronger dependence on the mapping, thus pointing to the existence of an optimal level of intermediate resolution.

We propose an open-boundary molecular dynamics method in which an atomistic system is in contact with an infinite particle reservoir at constant temperature, volume and chemical potential. In practice, following the Hamiltonian adaptive resolution strategy, the system is partitioned into a domain of interest and a reservoir of non-interacting, ideal gas, particles. An external potential, applied only in the interfacial region, balances the excess chemical potential of the system. To ensure that the size of the reservoir is infinite, we introduce a particle insertion/deletion algorithm to control the density in the ideal gas region. We show that it is possible to study non-equilibrium phenomena with this open-boundary molecular dynamics method. To this aim, we consider a prototypical confined liquid under the influence of an external constant density gradient. The resulting pressure-driven flow across the atomistic system exhibits a velocity profile consistent with the corresponding solution of the Navier-Stokes equation. In contrast to available computational methods in which external forces drive the system far from equilibrium, this approach conserves momentum and closely resembles experimental conditions. The presented method can be used to study various direct and indirect out-of-equilibrium conditions in complex molecular systems.

Coarse-grained (CG) models are often parametrized to reproduce one-dimensional structural correlation functions of an atomically-detailed model along the degrees of freedom governing each interaction potential. While cross correlations between these degrees of freedom inform the optimal set of interaction parameters, the correlations generated from the higher-resolution simulations are often too complex to act as an accurate proxy for the CG correlations. Instead, the most popular methods determine the interaction parameters iteratively, while assuming that individual interactions are uncorrelated. While these iterative methods have been validated for a wide range of systems, they also have disadvantages when parametrizing models for multi-component systems or when refining previously established models to better reproduce particular structural features. In this work, we propose two distinct approaches for the direct (i.e., non-iterative) parametrization of a CG model by adjusting the high-resolution cross correlations of an atomistic model in order to more accurately reflect correlations that will be generated by the resulting CG model. The derived models more accurately describe the low-order structural features of the underlying AA model, while necessarily generating inherently distinct cross correlations compared with the atomically-detailed reference model. We demonstrate the proposed methods for a one-site-per-molecule representation of liquid water, where pairwise interactions are incapable of reproducing the true tetrahedral solvation structure. We then investigate the precise role that distinct cross-correlation features play in determining the correct pair correlation functions, evaluating the importance of the placement of correlation features as well as the balance between features appearing in different solvation shells.

Computer simulations generate trajectories at a single, well-defined thermodynamic state point. Statistical reweighting offers the means to reweight static and dynamical properties to different equilibrium state points by means of analytic relations. We extend these ideas to non-equilibrium steady states by relying on a maximum path entropy formalism subject to physical constraints. Stochastic thermodynamics analytically relates the forward and backward probabilities of any pathway through the external non-conservative force, enabling reweighting both in and out of equilibrium. We avoid the combinatorial explosion of microtrajectories by systematically constructing pathways through Markovian transitions. We further identify a quantity that is invariant to dynamical reweighting, analogous to the density of states in equilibrium reweighting.

Polymer melts undergoing large deformation by uniaxial elongation are studied by molecular dynamics simulations of bead-spring chains in melts. Applying a primitive path analysis to strongly deformed polymer melts, the role of topological constrains in highly entangled polymer melts is investigated and quantified. We show that the over-all, large scale conformations of the primitive paths (PPs) of stretched chains follow affine deformation while the number and the distribution of entanglement points along the PPs do not. Right after deformation, PPs of chains retract in both directions parallel and perpendicular to the elongation. Upon further relaxation we observe a long-lived clustering of entanglement points. Together with the delayed relaxation time this leads to a metastable inhomogeneous distribution of topological constraints in the melts., Comment: 28 pages, 14 figures

We show here that molecular resolution is inherently hybrid in terms of relative separation: If molecules are close to each other, they must be characterized by a fine-grained (geometrically detailed) model, yet if molecules are far from each other, they may be described by a coarse-grained (isotropically simplified) model. We notably present an analytical expression for relating the two models by 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.

To study the cooling behavior and the glass transition of polymer melts in bulk and with free surfaces a coarse-grained weakly semi-flexible polymer model is developed. Based on a standard bead spring model with purely repulsive interactions an attractive potential between non-bonded monomers is added, such that the pressure of polymer melts is tuned to zero. Additionally, the commonly used bond bending potential [Everaers et al., Science 303, 823 (2004)] controlling the chain stiffness is replaced by a new bond bending potential. For this model, we show that the Kuhn length and the internal distances along the chains in the melt only very weakly depend on temperature, just as for typical experimental systems. The glass transition is observed by the temperature dependency of the melt density and the characteristic non-Arrhenius slowing down of the chain mobility. The model is set to allow for a fast switch between models, for which a wealth of data already exists., Comment: 6 pages, 5 figures; published version (including erratum)

Recently, we introduced Relative Resolution as a hybrid formalism for fluid mixtures [1]. The essence of this approach is that it switches molecular resolution in terms or relative separation: While nearest neighbors are characterized by a detailed fine-grained model, other neighbors are characterized by a simplified coarse-grained model. Once the two models are analytically connected with each other via energy conservation, Relative Resolution can capture the structural and thermal behavior of (nonpolar) multi-component and multi-phase systems across state space. The current work is a natural continuation of our original communication [1]. Most importantly, we present the comprehensive mathematics of Relative Resolution, basically casting it as a multipole approximation at appropriate distances; the current set of equations importantly applies for all systems (e.g, polar molecules). Besides, we continue examining the capability of our multiscale approach in molecular simulations, importantly showing that we can successfully retrieve not just the statics but also the dynamics of liquid systems. We finally conclude by discussing how Relative Resolution is the inherent variant of the famous "cell-multipole" approach for molecular simulations.

We demonstrate that hierarchical backmapping strategies incorporating generic blob-based models can equilibrate melts of high-molecular-weight polymers, described with chemically specific, atomistic, models. The central idea behind these strategies, is first to represent polymers by chains of large soft blobs (spheres) and efficiently equilibrate the melt on mesoscopic scale. Then, the degrees of freedom of more detailed models are reinserted step by step. The procedure terminates when the atomistic description is reached. Reinsertions are feasible computationally because the fine-grained melt must be re-equilibrated only locally. To develop the method, we choose a polymer with sufficient complexity. We consider polystyrene (PS), characterized by stereochemistry and bulky side groups. Our backmapping strategy bridges mesoscopic and atomistic scales by incorporating a blob-based, a moderately CG, and a united-atom model of PS. We demonstrate that the generic blob-based model can be parameterized to reproduce the mesoscale properties of a specific polymer -- here PS. The moderately CG model captures stereochemistry. To perform backmapping we improve and adjust several fine-graining techniques. We prove equilibration of backmapped PS melts by comparing their structural and conformational properties with reference data from smaller systems, equilibrated with less efficient methods., Comment: 18 pages

Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present computational tools for multiscale modeling developed and implemented within the ESPResSo++ package. These include the latest applications of the adaptive resolution scheme, the hydrodynamic interactions through a lattice Boltzmann solvent coupled to particle-based molecular dynamics, the implementation of the hierarchical strategy for equilibrating long-chained polymer melts and a heterogeneous spatial domain decomposition. The software design of ESPResSo++ has kept its highly modular C++ kernel with a Python user interface. Moreover, it was enhanced by automatic scripts parsing configurations from other established packages providing scientists with a rapid setup possibility for their simulations., Comment: 25 pages,8 figures, full research article

Syndiotactic polystyrene (sPS) exhibits complex polymorphic behavior upon crystallization. Computational modeling of polymer crystallization has remained a challenging task because the relevant processes are slow on the molecular time scale. We report herein a detailed characterization of sPS-crystal polymorphism by means of coarse-grained (CG) and atomistic (AA) modeling. The CG model, parametrized in the melt, shows remarkable transferability properties in the crystalline phase. Not only is the transition temperature in good agreement with atomistic simulations, it stabilizes the main $\alpha$ and $\beta$ polymorphs, observed experimentally. We compare in detail the propensity of polymorphs at the CG and AA level and discuss finite-size as well as box-geometry effects. All in all, we demontrate the appeal of CG modeling to efficiently characterize polymer-crystal polymorphism at large scale., Comment: 10 pages, 9 figures

We use computer simulations to study the relaxation of strongly deformed highly entangled polymer melts in the non-linear viscoelastic regime, focusing on anisotropic chain conformations after isochoric elongation. The Doi-Edwards tube model and its GLaMM extension, incorporating contour length fluctuation and convective constraint release, predict a retraction of the polymer chain extension in all directions, setting in immediately after deformation. This prediction has been challenged by experiment, simulation, and other theoretical studies, questioning the general validity of the tube concept. For very long chains we observe the initial contraction of the chain extension parallel and perpendicular to the stretching direction. However, the effect is significantly weaker than predicted by the GLaMM model. We also show that the first anisotropic term of an expansion of the 2D scattering function qualitatively agrees to predictions of the GLaMM model, providing an option for direct experimental tests., Comment: 6 pages, 3 figures, 7 references added

Many popular methods for the calculation of chemical potentials rely on the insertion of test particles into the target system. In the case of liquids and liquid mixtures, this procedure increases in difficulty upon increasing density or concentration, and the use of sophisticated enhanced sampling techniques becomes inevitable. In this work we propose an alternative strategy, spatially resolved thermodynamic integration, or SPARTIAN for short. Here, molecules are described with atomistic resolution in a simulation subregion, and as ideal gas particles in a larger reservoir. All molecules are free to diffuse between subdomains adapting their resolution on the fly. To enforce a uniform density profile across the simulation box, a single-molecule external potential is computed, applied, and identified with the difference in chemical potential between the two resolutions. Since the reservoir is represented as an ideal gas bath, this difference exactly amounts to the excess chemical potential of the target system. The present approach surpasses the high density/concentration limitation of particle insertion methods because the ideal gas molecules entering the target system region spontaneously adapt to the local environment. The ideal gas representation contributes negligibly to the computational cost of the simulation, thus allowing one to make use of large reservoirs at minimal expenses. The method has been validated by computing excess chemical potentials for pure Lennard-Jones liquids and mixtures, SPC and SPC/E liquid water, and aqueous solutions of sodium chloride. The reported results well reproduce literature data for these systems.

Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach which is a combination of an heterogeneity sensitive spatial domain decomposition with an \textit{a priori} rearrangement of subdomain-walls. Within this approach, the theoretical modeling and scaling-laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. These two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase separated binary Lennard-Jones fluid., Comment: 14 pages, 12 figures

Path integral-based simulation methodologies play a crucial role for the investigation of nuclear quantum effects by means of computer simulations. However, these techniques are significantly more demanding than corresponding classical simulations. To reduce this numerical effort, we recently proposed a method, based on a rigorous Hamiltonian formulation, which restricts the quantum modeling to a small but relevant spatial region within a larger reservoir where particles are treated classically. In this work, we extend this idea and show how it can be implemented along with state-of-the-art path integral simulation techniques, such as ring polymer and centroid molecular dynamics, which allow the approximate calculation of both quantum statistical and quantum dynamical properties. To this end, we derive a new integration algorithm which also makes use of multiple time-stepping. The scheme is validated via adaptive classical--path-integral simulations of liquid water. Potential applications of the proposed multiresolution method are diverse and include efficient quantum simulations of interfaces as well as complex biomolecular systems such as membranes and proteins.

The determination of potentials of mean force for solute insertion in a membrane by means of all-atom molecular dynamics simulations is often hampered by sampling issues. A multiscale approach to conformational sampling was recently proposed by Bereau and Kremer (2016). It aims at accelerating the sampling of the atomistic conformational space by means of a systematic backmapping of coarse-grained snapshots. In this work, we first analyze the efficiency of this method by comparing its predictions for propanol insertion into a 1,2-Dimyristoyl-sn-glycero-3-phosphocholine membrane (DMPC) against reference atomistic simulations. The method is found to provide accurate results with a gain of one order of magnitude in computational time. We then investigate the role of the coarse-grained representation in affecting the reliability of the method in the case of a 1,2-Dioleoyl-sn-glycero-3-phosphocholine membrane (DOPC). We find that the accuracy of the results is tightly connected to the presence a good configurational overlap between the coarse-grained and atomistic models---a general requirement when developing multiscale simulation methods., Comment: 6 pages, 5 figures

Polymer properties are inherently multi-scale in nature, where delicate local interaction details play a key role in describing their global conformational behavior. In this context, deriving coarse-grained (CG) multi-scale models for polymeric liquids is a non-trivial task. Further complexities arise when dealing with copolymer systems with varying microscopic sequences, especially when they are of an amphiphilic nature. In this work, we derive a segment-based generic CG model for amphiphilic copolymers consisting of repeat units of hydrophobic (methylene) and hydrophilic (ethylene oxide) monomers. The system is a simulation analogue of polyacetal copolymers [Samanta et al., Macromolecules 49, 1858 (2016)]. The CG model is found to be transferable over a wide range of copolymer sequences and also to be consistent with existing experimental data.

The partitioning of small molecules in cell membranes---a key parameter for pharmaceutical applications---typically relies on experimentally-available bulk partitioning coefficients. Computer simulations provide a structural resolution of the insertion thermodynamics via the potential of mean force, but require significant sampling at the atomistic level. Here, we introduce high-throughput coarse-grained molecular dynamics simulations to screen thermodynamic properties. This application of physics based models in a large-scale study of small molecules establishes linear relationships between partitioning coefficients and key features of the potential of mean force. This allows us to predict the structure of the insertion from bulk experimental measurements for more than 400,000 compounds. The potential of mean force hereby becomes an easily accessible quantity---already recognized for its high predictability of certain properties, e.g., passive permeation. Further, we demonstrate how coarse graining helps reduce the size of chemical space, enabling a hierarchical approach to screening small molecules., Comment: 8 pages, 6 figures. Typos fixed, minor corrections

Recent theoretical studies found that mixtures of active and passive colloidal particles phase separate but only at very high activity ratio. The high value poses serious obstacles for experimental exploration of this phenomenon. Here we show using simulations that when the active and passive particles are polymers, the critical activity ratio decreases with the polymer length. This not only facilitates the experiments but also has implications on the DNA organization in living cell nuclei. Entropy production can be used as an accurate indicator of this non-equilibrium phase transition.

We present large-scale molecular dynamics simulations for a coarse-grained model of polymer melts in equilibrium. From detailed Rouse mode analysis we show that the time-dependent relaxation of the autocorrelation function (ACF) of modes $p$ can be well described by the effective stretched exponential function due to the crossover from Rouse to reptation regime. The ACF is independent of chain sizes $N$ for $N/p

In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is needed in the active site to capture the chemistry of substrate binding. Global properties of the rest of the protein also play an essential role, determining the structure and fluctuations of the binding site; however, these can be modelled on a coarser level. Similarly, in the most computationally efficient scheme only the solvent hydrating the active site requires atomistic detail. We present a methodology to couple atomistic and coarse-grained protein models, while solvating the atomistic part of the protein in atomistic water. This allows a free choice of which protein and solvent degrees of freedom to include atomistically, without loss of accuracy in the atomistic description. This multi-resolution methodology can successfully model stable ligand binding, and we further confirm its validity via an exploration of system properties relevant to enzymatic function. In addition to a computational speedup, such an approach can allow the identification of the essential degrees of freedom playing a role in a given process, potentially yielding new insights into biomolecular function.

A strategy is developed for generating equilibrated high molecular-weight polymer melts described with microscopic detail by sequentially backmapping coarse-grained (CG) configurations. The microscopic test model is generic but retains features like hard excluded volume interactions and realistic melt densities. The microscopic representation is mapped onto a model of soft spheres with fluctuating size, where each sphere represents a microscopic subchain with $N_{\rm b}$ monomers. By varying $N_{\rm b}$ a hierarchy of CG representations at different resolutions is obtained. Within this hierarchy, CG configurations equilibrated with Monte Carlo at low resolution are sequentially fine-grained into CG melts described with higher resolution. A Molecular Dynamics scheme is employed to slowly introduce the microscopic details into the latter. All backmapping steps involve only local polymer relaxation thus the computational efficiency of the scheme is independent of molecular weight, being just proportional to system size. To demonstrate the robustness of the approach, microscopic configurations containing up to $n=1000$ chains with polymerization degrees $N=2000$ are generated and equilibration is confirmed by monitoring key structural and conformational properties. The extension to much longer chains or branched polymers is straightforward.

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.

Macromolecular solubility in solvent mixtures often exhibit striking and paradoxical nature. For example, when two well miscible poor solvents for a given polymer are mixed together, the same polymer may swell within intermediate mixing ratios. We combine computer simulations and theoretical arguments to unveil the first microscopic, generic origin of this collapse-swelling-collapse scenario. We show that this phenomenon naturally emerges at constant pressure in mixtures of purely repulsive components, especially when a delicate balance of the entropically driven depletion interactions is achieved.

We present a detailed study of the static and dynamic behavior of long semiflexible polymer chains in a melt. Starting from previously obtained fully equilibrated high molecular weight polymer melts [{\it Zhang et al.} ACS Macro Lett. 3, 198 (2014)] we investigate their static and dynamic scaling behavior as predicted by theory. We find that for semiflexible chains in a melt, results of the mean square internal distance, the probability distributions of the end-to-end distance, and the chain structure factor are well described by theoretical predictions for ideal chains. We examine the motion of monomers and chains by molecular dynamics simulations using the ESPResSo++ package. The scaling predictions of the mean squared displacement of inner monomers, center of mass, and relations between them based on the Rouse and the reptation theory are verified, and related characteristic relaxation times are determined. Finally we give evidence that the entanglement length $N_{e,PPA}$ as determined by a primitive path analysis (PPA) predicts a plateau modulus, $G_N^0=\frac{4}{5}(\rho k_BT/N_e)$, consistent with stresses obtained from the Green-Kubo relation. These comprehensively characterized equilibrium structures, which offer a good compromise between flexibility, small $N_e$, computational efficiency, and small deviations from ideality provide ideal starting states for future non-equilibrium studies., Comment: 13 pages, 10 figures, to be published in J. Chem. Phys. (2016)

We present a coarse-graining strategy that we test for aqueous mixtures. The method uses pair-wise cumulative coordination as a target function within an iterative Boltzmann inversion (IBI) like protocol. We name this method coordination iterative Boltzmann inversion ($\mathcal {C}-$IBI). While the underlying coarse-grained model is still structure based and, thus, preserves pair-wise solution structure, our method also reproduces solvation thermodynamics of binary and/or ternary mixtures. Additionally, we observe much faster convergence within $\mathcal {C}-$IBI compared to IBI. To validate the robustness, we apply $\mathcal {C}-$IBI to study test cases of solvation thermodynamics of aqueous urea and a triglycine solvation in aqueous urea.

Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation methodology, model errors may lead to inconsistencies between simulated and reference (e.g., from experiments or higher-level simulations) observables. To bound the microscopic information generated by computer simulations within reference measurements, we propose a method that reweights the microscopic transitions of the system to improve consistency with a set of coarse kinetic observables. The method employs the well-developed Markov state modeling framework to efficiently link microscopic dynamics with long-time scale constraints, thereby consistently addressing a wide range of time scales. To emphasize the robustness of the method, we consider two distinct coarse-grained models with significant kinetic inconsistencies. When applied to the simulated conformational dynamics of small peptides, the reweighting procedure systematically improves the time scale separation of the slowest processes. Additionally, constraining the forward and backward rates between metastable states leads to slight improvement of their relative stabilities and, thus, refined equilibrium properties of the resulting model. Finally, we find that difficulties in simultaneously describing both the simulated data and the provided constraints can help identify specific limitations of the underlying simulation approach.

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.

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.