We investigate the addition of stiffness to the lattice model of hydrogen-bonded polymers in two and three dimensions. We find that, in contrast to polymers that interact via a homogeneous short-range interaction, the collapse transition is unchanged by any amount of stiffness: this supports the physical argument that hydrogen bonding already introduces an effective stiffness. Contrary to possible physical arguments, favouring bends in the polymer does not return the model's behaviour to that comparable to the semi-flexible homogeneous interaction model, where the canonical $θ$-point occurs for a range of parameter values. In fact, for sufficiently large bending energies the crystal phase disappears altogether, and no phase transition of any type occurs. We also compare the order-disorder transition from the globule phase to crystalline phase in the semi-flexible homogeneous interaction model to that for the fully-flexible hybrid model with both hydrogen and non-hydrogen like interactions. We show that these phase transitions are of the same type and are a novel polymer critical phenomena in two dimensions. That is, it is confirmed that in two dimensions this transition is second-order, unlike in three dimensions where it is known to be first order. We also estimate the crossover exponent and show that there is a divergent specific heat, finding $ϕ=0.7(1)$ or equivalently $α=0.6(2)$. This is therefore different from the $θ$ transition, for which $α=-1/3$.
A coarse-grained multi-blob description of polymer solutions is presented, based on soft, transferable effective interactions between bonded and non-bonded blobs. The number of blobs is chosen such that the blob density does not exceed their overlap threshold, allowing polymer concentrations to be explored deep into the semi-dilute regime. This quantitative multi-blob description is shown to preserve known scaling laws of polymer solutions and provides accurate estimates of amplitudes, while leading to orders of magnitude increase of simulation efficiency and allowing analytic calculations of …
Properties of cylindrical quantum wires are analysed in this paper. Energies of elementary excitations as well as one-particle wave functions were found for mentioned structure. For cylindrical quantum wires the temperature of phase transition was found. The behaviour of electric susceptibility in paraelectric phase was investigated.
We address the relaxation dynamics in hydrogen-bonded super-cooled liquids near the glass transition, measured via Broad-Band Dielectric Spectroscopy (BDS). We propose a theory based on decomposing the relaxation of the macroscopic dipole moment into contributions from hydrogen bonded clusters of $s$ molecules, with $s_{min}\le s \le s_{max}$. The existence of $s_{max}$ is due to dynamical arrest and its value may depend on the cooling protocol and on the aging time. The existence of $s_{max}$ is translated into a sum-rule on the concentrations of clusters of size $s$. We construct the statist…
We improve a lattice model of water introduced by Sastry, Debenedetti, Sciortino, and Stanley to give insight on experimental thermodynamic anomalies in supercooled phase, taking into account the correlations between intra-molecular orientational degrees of freedom. The original Sastry et al. model including energetic, entropic and volumic effect of the orientation-dependent hydrogen bonds (HBs), captures qualitatively the experimental water behavior, but it ignores the geometrical correlation between HBs. Our mean-field calculation shows that adding these correlations gives a more water-like …
In this paper I describe a specialized algorithm for anisotropic diffusion determined by a field of transition rates. The algorithm can be used to describe some interesting forms of diffusion that occur in the study of proton motion in a network of hydrogen bonds. The algorithm produces data that require a nonstandard method of spectral analysis which is also developed here. Finally, I apply the algorithm to a simple specific example.
We introduce a novel coarse-grained bead-spring model for flexible polymers to systematically examine the effects of an adjusted bonded potential on the formation and stability of structural macrostates in a thermal environment. The density of states obtained in advanced replica-exchange Monte Carlo simulations is analyzed by employing the recently developed generalized microcanonical inflection-point analysis method, which enables the identification of diverse structural phases and the construction of a suitably parameterized hyperphase diagram. It reveals that icosahedral phases dominate for…
The axiomatic theory of ideally glassy networks, which has proved effective in describing phase diagrams and properties of chalcogenide and oxide glasses and their foreign interfaces, is broadened here to include intermolecular interactions in hydrogen-bonded polyalcohols such as glycerol, monosaccharides (glucose), and the optimal bioprotective hydrogen-bonded disaccharide networks formed from trehalose. The methods of Lagrangian mechanics and Maxwellian scaffolds are useful at the molecular level when bonding hierarchies are characterized by constraint counting similar to the chemical method…
The effect on the nematic to smectic-A transition in octylcyanobiphenyl (8CB) due to dispersions of hydrogen-bonded silica (aerosil) particles is characterized with high-resolution x-ray scattering. The particles form weak gels in 8CB creating a quenched disorder that replaces the transition with the growth of short range smectic correlations. The correlations include thermal critical fluctuations that dominate at high temperatures and a second contribution that quantitatively matches the static fluctuations of a random field system and becomes important at low temperatures.
In addition to the gauge charges, a new charge degree of freedom is found in the deconfined phase in the lattice Ising gauge theory. While applying to the hydrogen-bonded ferroelectrics, the new charge is essentially the electric charge, leading to the divergent dielectric susceptibility. The new degree of freedom paves an experimentally accessible way to identify the deconfined phase in the lattice Ising gauge theory.
Extensive molecular dynamics computer simulations have been conducted for ethanol-water liquid mixtures in the water-rich side of the composition range, with 10, 20 and 30 mol % of the alcohol, at temperatures between room temperature and the experimental freezing point of the given mixture. All-atom type (OPLS) interatomic potentials have been assumed for ethanol, in combination with two kinds of rigid water models (SPC/E and TIP4P/2005). Both combinations have provided excellent reproductions of the experimental X-ray total structure factors at each temperature; this provided a strong basis …
Hydrogen bonding to chloride ions has been frequently discussed over the past 5 decades. Still, the possible role of such secondary intermolecular bonding interactions in hydrogen bonded networks has not been investigated in any detail. Here we consider computer models of concentrated aqueous LiCl solutions and compute usual hydrogen bond network characteristics, such as distributions of cluster sizes and of cyclic entities, both for models that take and do not take chloride ions into account. During the analysis of hydrogen bonded rings, a significant amount of 'solvent separated anion pairs'…
New X-ray and neutron diffraction experiments have been performed on ethanol-water mixtures as a function of decreasing temperature, so that such diffraction data are now available over the entire composition range. Extensive molecular dynamics simulations show that the all-atom interatomic potentials applied are adequate for gaining insight of the hydrogen bonded network structure, as well as of its changes on cooling. Various tools have been exploited for revealing details concerning hydrogen bonding, like determining H-bond acceptor and donor sites, calculating cluster size distributions an…
Single-chain nanoparticles (SCNP) are a new class of bio and soft-matter polymeric objects in which a fraction of the monomers are able to form equivalently intra- or inter-polymer bonds. Here we numerically show that a fully-entropic gas-liquid phase separation can take place in SCNP systems. Control over the discontinuous (first-order) change -- from a phase of independent diluted (fully-bonded) polymers to a phase in which polymers entropically bind to each other to form a (fully-bonded) polymer network -- can be achieved by a judicious design of the patterns of reactive monomers along the …
Structures resembling semiclathrates probably arise in liquid aqueous solutions of piperidine at the amine mole fraction below 0.03. With the increasing concentration, the structures gradually decay, but the 1:1 complexes of piperidine with water remain linked one to another through the O-H...O bonds between the hydration water molecules. A periodic order of the bicontinuous microemulsion type occurs in the range of the mole fractions from 0.08 to 0.5. In the piperidine-rich mixtures, the 1:1 complexes are dispersed uniformly in the amine. Relatively low stabilization energy of these complexes…
The coupling behavior of time scales of structural relaxation is investigated on the basis of five different response functions for 1,2,6-hexanetriol, a hydrogen-bonded liquid with a minor secondary contribution, and 2,6,10,15,19,23-hexamethyl-tetracosane (squalane), a van der Waals bonded liquid with a prominent secondary relaxation process. Time scales of structural relaxation are derived as inverse peak frequencies for each investigated response function. For 1,2,6-hexanetriol, the time-scale indices are temperature-independent, while a decoupling of time scales is observed for squalane in …
We present results for a lattice model of bio-polymers where the type of $β$-sheet formation can be controlled by different types of hydrogen bonds depending on the relative orientation of close segments of the polymer. Tuning these different interaction strengths leads to low-temperature structures with different types of orientational order. We perform simulations of this model and so present the phase diagram, ascertaining the nature of the phases and the order of the transitions between these phases.
We investigate a lattice model of polymers where the nearest-neighbour monomer-monomer interaction strengths differ according to whether the local configurations have so-called ``hydrogen-like'' formations or not. If the interaction strengths are all the same then the classical $θ$-point collapse transition occurs on lowering the temperature, and the polymer enters the isotropic liquid-drop phase known as the collapsed globule. On the other hand, strongly favouring the hydrogen-like interactions give rise to an anisotropic folded (solid-like) phase on lowering the temperature. We use Monte Car…
Recently it has been shown that a two-dimensional model of self-attracting polymers based on attracting segments displays two phase transitions, a theta-like collapse between swollen polymers and a globular state and another between the globular state and a polymer crystal. On the other hand, the canonical model based on attracting monomers on lattice sites displays only one: the standard tricritical theta collapse transition. Here we show that by considering both models with the addition of stiffness the two models display the same generic phase diagram. In fact we claim that any two-dimensio…
We visualize entanglements in polymer melts using molecular dynamics simulation. A bead at an entanglement interacts persistently for long times with the non-bonded beads (those excluding the adjacent ones in the same chain). The interaction energy of each bead with the non-bonded beads is averaged over a time interval $τ$ much longer than microscopic times but shorter than the onset time of tube constraints $τ_{\rm e}$. Entanglements can then be detected as hot spots consisting of several beads with relatively large values of the time-averaged interaction energy. We next apply a shear flow wi…
Tuning the heat flow is fundamentally important for the design of advanced functional materials. Here, polymers are of particular importance because they provide different pathways for the energy transfer. More specifically, the heat flow between two covalently bonded monomers is over 100 times faster than between the two non-bonded monomers interacting via van der Waals (vdW) forces. Therefore, the delicate balance between these two contributions often provide a guiding tool for the tunability in thermal transport coefficient k of the polymeric materials. Traditionally most studies have inves…
In this work we present the general phase behavior of short tubelike flexible polymers. The geometric thickness constraint is implemented through the concept of the global radius of curvature. We use sophisticated Monte Carlo sampling methods to simulate small bead-stick polymer models with Lennard-Jones interaction among non-bonded monomers. We analyze energetic fluctuations and structural quantities to classify conformational pseudophases. We find that the tube thickness influences the thermodynamic behavior of simple tubelike polymers significantly, i.e., for given temperature, the formatio…
We have investigated the hydrogen-bonded structures in liquid methanol and a 7:3 mole fraction aqueous solution using classical Molecular Dynamics simulations at 298K and ambient pressure. We find that, in contrast to recent predictions from X-ray emission studies, the hydrogen-bonded structure in liquid methanol is dominated by chain and small ring structures. In the methanol-rich solution, we find evidence of micro-immiscibility, supporting recent conclusions derived from neutron diffraction data.
Pure FENE Bond Potential for Soft Matter and Biological Simulations: Theory, HOOMD-blue Implementation, and Applications to Polymer, Colloidal, and Membrane Systems
We perform an extensive combinatorial search for optimal nanostructured hydrogen storage materials among various metal-decorated polymers using first-principles density-functional calculations. We take into account the zero-point vibration as well as the pressure- and temperature-dependent adsorption-desorption probability of hydrogen molecules. An optimal material we identify is Ti-decorated cis-polyacetylene with reversibly usable gravimetric and volumetric density of 7.6 weight percent and 63 kg/m^3 respectively near ambient conditions. We also propose ``thermodynamically usable hydrogen ca…
Limited-valency colloidal particles can self-assemble into polymeric structures analogous to molecules. While their structural equilibrium properties have attracted wide attention, insight into their dynamics has proven challenging. Here, we investigate the polymerization dynamics of semiflexible polymers in two dimensions (2D) by direct observation of assembling divalent particles, bonded by critical Casimir forces. The reversible critical Casimir force creates living polymerization conditions with tunable chain dissociation, association and bending rigidity. We find that unlike dilute polyme…
Structure, Dynamics and Hydrogen Transport in Amorphous Polymers: An Analysis of the Interplay Between Free Volume Element Distribution and Local Segmental Dynamics from Molecular Dynamics Simulations
Applications of commodity polymers are often hindered by their low thermal conductivity. In these systems, going from the standard polymers dictated by weak van der Waals interactions to biocompatible hydrogen bonded smart polymers, the thermal transport coefficient k varies between 0.1 - 0.4 W/Km. Combining all-atom molecular dynamics simulations with some experiments, we study thermal transport and its link to the elastic response of commodity plastics. We find that there exists a maximum attainable stiffness (or sound wave velocity), thus providing an upper bound of k for these solid polyme…
The problem of the helix-coil transition of biopolymers in explicit solvents, like water, with the ability for hydrogen bonding with solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide Chains. Besides the regular helix-coil transition, an additional coil-helix or reentrant transition is also found at lower temperatures. The reentrant transition arises due to competition between polymer-polymer and polymer-water hydrogen bonds. The balance between the two types of hydrogen bonding can be shifted to either direction through changes not only…
Aqueous mixtures of 1-propanol have been investigated by high-energy synchrotron X-ray diffraction upon cooling. X-ray weighted total scattering structure factors of 6 mixtures, from 8 mol% to 89 mol% alcohol content, as well as that of pure 1-propanol are reported from room temperature down to the freezing points of the liquids. Molecular dynamics simulations have been performed, in order to interpret measured data. The all atom OPLS-AA potential model was used for 1-propanol, combined with both the SPC/E and the TIP4P/2005 water models: both combinations provide a semi-quantitative descripti…
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 d…
The glass transition in hydrogen-bonded glass formers differs from the glass transition in other glass formers. The Eshelby rearrangements of the highly viscous flow are superimposed by strongly asymmetric hydrogen bond rupture processes, responsible for the excess wing. Their influence on the shear relaxation spectrum is strong in glycerol and close to zero in PPE, reflecting the strength of the hydrogen bond contribution to the high frequency shear modulus. A recent theory of the highly viscous flow enables a quantitative common description of the relaxation spectra in shear, linear and non-…
A grand challenge in designing polymeric materials is to tune their properties by macromolecular engineering. In this context, one of the drawbacks that often limits broader applications under high temperature conditions is their poor thermal conductivity $κ$. Using molecular dynamics simulations, we establish a structure-property relationship in hydrogen bonded polymer blends for possible improvement of $κ$. For this purpose, we investigate two experimentally relevant hydrogen bonded systems -- one system consists of short poly({N}-acryloyl piperidine) (PAP) blended with longer chains of poly…
Understanding the role of self-propulsion on the conformational properties of active filamentous objects has relevance in biology. In this context, we consider a flexible bead-spring model polymer for which along with both attractive and repulsive interactions among the non-bonded monomers, activity for each bead works along its intrinsic direction of self-propulsion. We study its kinetics in the overdamped limit, following a quench from good to poor solvent condition. We observe that with low activities, though the kinetic pathways remain similar, the scaling exponent for the relaxation time …
Liquid water is one of the most studied substances, yet many of its properties are difficult to rationalize. The uniqueness of water is rooted in the dynamic network of hydrogen-bonded molecules with relaxation time constants of about one picosecond. Terahertz fields oscillate on a picosecond timescale and are inherently suited to study water. Recent advances in non-linear terahertz spectroscopy have revealed large signals from water, which have been interpreted with different, sometimes competing, theoretical models. Here we show that the non-linear transmission of liquid water at ~1 THz is e…
Cells possess non-membrane-bound bodies, many of which are now understood as phase-separated condensates. One class of such condensates is composed of two polymer species, where each consists of repeated binding sites that interact in a one-to-one fashion with the binding sites of the other polymer. Previous biologically-motivated modeling of such a two-component system surprisingly revealed that phase separation is suppressed for certain combinations of numbers of binding sites. This phenomenon, dubbed the "magic-number effect", occurs if the two polymers can form fully-bonded small oligomers…
