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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.

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

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

We study the behavior of five proteins at the air-water and oil-water interfaces by all-atom molecular dynamics. The proteins are found to get distorted when pinned to the interface. This behavior is consistent with the phenomenological way of introducing the interfaces in a coarse-grained model through a force that depends on the hydropathy indices of the residues. Proteins couple to the oil-water interface stronger than to the air- water one. They diffuse slower at the oil-water interface but do not depin from it, whereas depinning events are observed at the other interface. The reduction of the disulfide bonds slows the diffusion down., Comment: 13 pages, 10 figures

We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain simultaneously in the two chains. We have identified about 900 entangled systems in the Protein Data Bank and provided a more detailed analysis for several of them. We argue that entanglement enhances the thermodynamic stability of the system but it may have other functions: burying the hydrophobic residues at the interface, and increasing the DNA or RNA binding area. We also study the folding and stretching properties of the knotted dimeric proteins MJ0366, YibK and bacteriophytochrome. These proteins have been studied theoretically in their monomeric versions so far. The dimers are seen to separate on stretching through the tensile mechanism and the characteristic unraveling force depends on the pulling direction., Comment: 11 figures, 16 pages

We use a coarse-grained model to study the conformational changes in two barley proteins, LTP1 and its ligand adduct isoform LTP1b, that result from their adsorption to the air-water interface. The model introduces the interface through hydropathy indices. We justify the model by all-atom simulations. The choice of the proteins is motivated by making attempts to understand formation and stability of foam in beer. We demonstrate that both proteins flatten out at the interface and can make a continuous stabilizing and denser film. We show that the degree of the flattening depends on the protein -- the layers of LTP1b should be denser than those of LTP1 -- and on the presence of glycation. It also depends on the number ($\le 4$) of the disulfide bonds in the proteins. The geometry of the proteins is sensitive to the specificity of the absent bonds. We provide estimates of the volume of cavities of the proteins when away from the interface., Comment: 18 pages, 18 figures

Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally distinct from those identified for folding at its optimal temperature. In particular, for shallowly knotted proteins, folding usually involves formation of two loops whereas unfolding through high-temperature heating is dominated by untying of single loops. Untying the knots is found to generally precede unfolding unless the protein is deeply knotted and the heating temperature exceeds a threshold value. We then use a phenomenological model of the air-water interface to show that such an interface can untie shallow knots, but it can also make knots in proteins that are natively unknotted., Comment: 7 figures

The mechanical properties of polymer knots under stretching in a bad or good solvent are investigated by applying a given force $F$ to a point of the knot while keeping another point fixed. The Monte Carlo sampling of the polymer conformations on a simple cubic lattice is performed using a variant of the Wang-Landau algorithm. The results of the calculations of the specific energy, specific heat capacity and gyration radius for several knot topologies show a general trend in the behavior of short polymer knots with lengths up to seventy lattice units. At low tensile force $F$, knots can be found either in a compact or an extended phase, depending if the temperature is low or high. At any temperature, with increasing values of the force $F$, a polymer knot undergoes a phase transition to a stretched state. This transition is characterized by a strong peak in the heat capacity. There is also a minor peak, which corresponds to a transition occurring at low temperatures when the conformations of polymers in the stretched phase become swollen with increasing temperatures. It is also shown that the behavior of short polymer rings is strongly influenced by topological effects. The limitations in the number of accessible energy states due to topological constraints is particularly evident in knots of small size and such that their minimum number of crossing according to the Rolfsen knot table is high. An example is provided by a cinquefoil knot $5_1$ with a length of only fifty lattice units. The thermal and mechanical properties of knots that can be represented with diagrams having the same minimum number of crossings, are very similar. The size effects on the behavior of polymer knots have been analyzed too. Surprisingly, it is found that topological effects fade out very fast with increasing polymer length., Comment: 13 pages, 12 figures

The subject of this work is a three-dimensional topological field theory with a non-semisimple group of gauge symmetry with observables consisting in the holonomies of connections around three closed loops. The connections are a linear combination of gauge potentials with coefficients containing a set of one-dimensional scalar fields. It is checked that these observables are both metric independent and gauge invariant. The gauge invariance is achieved by requiring non-trivial gauge transformations in the scalar field sector. This topological field theory is solvable and has only a relevant amplitude which has been computed exactly. From this amplitude it is possible to isolate a topological invariant which is Milnor's triple linking invariant. The topological invariant obtained in this way is in the form of a sum of multiple contour integrals. The contours coincide with the trajectories of the three loops mentioned before. The introduction of the one-dimensional scalar field is necessary in order to reproduce correctly the particular path ordering of the integration over the contours which is present in the triple Milnor linking coefficient. This is the first example of a local topological gauge field theory that is solvable and can be associated to a topological invariant of the complexity of the triple Milnor linking coefficient., Comment: 9 pages, no figures, LaTeX + RevTeX 4

The field theory approach to the statistical mechanics of a system of N polymer rings linked together is generalized to the case of links that have a fixed number $2s$ of maxima and minima. Such kind of links are called plats and appear for instance in the DNA of living organisms. The topological states of the link are distinguished using the Gauss linking number. This is a relatively weak link invariant in the case of a general link, but its efficiency improves when $2s-$plats are considered. It is proved that, if we restrict ourselves to $2s-$plat conformations, the field theoretical model established here is able to take into account also the interactions of topological origin involving three chains simultaneously. It is shown that these three-body interactions have nonvanishing contributions when three or more rings are entangled together, enhancing for instance the attractive forces between monomers. The model can be used to study the statistical mechanics of polymers in confined geometries, for instance when $2s$ extrema of a few polymer rings are attached to membranes. Its partition function is mapped here into that of a multi-layer electron gas. Such quasi-particle systems are studied in connection with several interesting applications, including high-$T_c$ superconductivity and topological quantum computing. At the end an useful connection with the cosh-Gordon equation is shown., Comment: 35 pages, 8 figures. arXiv admin note: substantial text overlap with arXiv:1304.5980

In the first part of this work a summary is provided of some recent experiments and theoretical results which are relevant in the research of systems of polymer rings in nontrivial topological conformations. Next, some advances in modeling the behavior of single polymer knots are presented. The numerical simulations are performed with the help of the Wang-Landau Monte Carlo algorithm. To sample the polymer conformation a set of random transformations called pivot moves is used. The crucial problem of preserving the topology of the knots after each move is tackled with the help of two new techniques which are briefly explained. As an application, the results of an investigation of the effects of topology on the thermal properties of polymer knots is reported. In the end, original results are discussed concerning the use of parallelized codes to study polymers knots composed by a large number of segments within the Wang-Landau approach., Comment: 14 pages, 7 figures, proceedings of the conference ISMC 2013, 15-19 September 2013, Rome, Italy

In mathematics there is a wide class of knot invariants that may be expressed in the form of multiple line integrals computed along the trajectory C describing the spatial conformation of the knot. In this work it is addressed the problem of evaluating invariants of this kind in the case in which the knot is discrete, i.e. its trajectory is constructed by joining together a set of segments of constant length. Such discrete knots appear almost everywhere in numerical simulations of systems containing one dimensional ring-shaped objects. Examples are polymers, the vortex lines in fluids and superfluids like helium and other quantum liquids. Formally, the trajectory of a discrete knot is a piecewise smooth curve characterized by sharp corners at the joints between contiguous segments. The presence of these corners spoils the topological invariance of the knot invariants considered here and prevents the correct evaluation of their values. To solve this problem, a smoothing procedure is presented, which eliminates the sharp corners and transforms the original path C into a curve that is everywhere differentiable. The procedure is quite general and can be applied to any discrete knot defined off or on lattice. This smoothing algorithm is applied to the computation of the Vassiliev knot invariant of degree 2 denoted here with the symbol r(C). This is the simplest knot invariant that admits a definition in terms of multiple line integrals. For a fast derivation of r(C), it is used a Monte Carlo integration technique. It is shown that, after the smoothing, the values of r(C) may be evaluated with an arbitrary precision. Several algorithms for the fast computation of the Vassiliev knot invariant of degree 2 are provided., Comment: 35 pages, 13 figures, LaTeX + RevTeX 4.1, a mistake in the name of one of the authors has been corrected

In this work the thermodynamic properties of short polymer knots (up to 120 segments) defined on a simple cubic lattice are studied with the help of the Wang-Landau Monte Carlo algorithm. The sampling process is performed using pivot transformations starting from a given seed conformation. Both cases of short-range attractive and repulsive interactions acting on the monomers are considered. The properties of the specific energy, heat capacity and gyration radius of several knots are discussed. It is found that the heat capacity exhibits a sharp peak. If the interactions are attractive, similar peaks have been observed also in single open chains and have been related to the transition from a frozen crystallite state to an expanded coil state. Some other peculiarities of the behavior of the analyzed observables are presented, like for instance the increasing or decreasing of the knot specific energy at high temperatures with increasing polymer lengths depending if the interactions are attractive or repulsive. Besides the investigation of the thermodynamics of polymer knots, the second goal of this paper is to introduce a method for distinguishing the topology of a knot based on a topological invariant which is in the form of multiple contour integrals and explicitly depends on the physical trajectory of the knot. The chosen invariant is related to the second coefficient of the Conway polynomial. It has been first isolated from the amplitudes of a Chern-Simons field theory with gauge group SU(N). It is shown that this invariant is very reliable in distinguishing the topology of polymer knots. One of the advantages of the proposed approach is that it allows to reduce the number of samples needed by the Wang-Landau algorithm. Some solutions to speed up the calculations exploiting Monte Carlo integration techniques are developed., Comment: 18 pages, 15 figures, LaTeX + RevTeX 4, a small misprint in fig. 9 corrected, some new references added

Anyon systems are studied in connection with several interesting applications including high $T_C$ superconductivity and topological quantum computing. In this work we show that these systems can be realized starting from directed polymers braided together to form a nontrivial link configuration belonging to the topological class of plats. The statistical sum of a such plat is related here to the partition function of a two-component anyon gas. The constraints that preserve the topological configuration of the plat are imposed on the polymer trajectories using the so-called Gauss linking number, a topological invariant that has already been well studied in polymer physics. Due to these constraints, short-range forces act on the monomers or, equivalently, on the anyon quasiparticles in a way that closely resembles the appearance of reaction forces in the constrained systems of classical mechanics. If the polymers are homogeneous, the anyon system reaches a self-dual point, in which these forces vanish exactly. A class of self-dual solutions that minimize the energy of the anyons is derived. The two anyon gas discussed here obeys an abelian statistics, while for quantum computing it is known that nonabelian anyons are necessary. However, this is a limitation due to the use of the Gauss linking invariant to impose the topological constraints, which is a poor topological invariant and is thus unable to capture the nonabelian characteristics of the braided polymer chains. A more refined treatment of the topological constraints would require more sophisticated topological invariants, but so far their application to the statistical mechanics of linked polymers is an open problem., Comment: title changed, several references added, typos corrected, text improved. 42 pages, 5 figures

The statistical mechanics of single polymer knots is studied using Monte Carlo simulations. The polymers are considered on a cubic lattice and their conformations are randomly changed with the help of pivot transformations. After each transformation, it is checked if the topology of the knot is preserved by means of a method called pivot algorithm and excluded area (in short PAEA) and described in a previous publication of the authors. As an application of this method the specific energy, the radius of gyration and heat capacity of a few types of knots are computed. The case of attractive short-range forces is investigated. The sampling of the energy states is performed by means of the Wang-Landau algorithm. The obtained results show that the specific energy and heat capacity increase with increasing knot complexity as in the case of repulsive interactions. The data about the gyration radius allow to estimate the size of the polymer knots at different temperatures., Comment: 8 pages, 2 figures, LaTeX + appolb.cls, Proceedings of the 25th Marian Smoluchowski Symposium on Statistical Physics, 9--13 September 2012, Cracow

The topological effects on the thermal properties of several knot configurations are investigated using Monte Carlo simulations. In order to check if the topology of the knots is preserved during the thermal fluctuations we propose a method that allows very fast calculations and can be easily applied to arbitrarily complex knots. As an application, the specific energy and heat capacity of the trefoil, the figure-eight and the $8_1$ knots are calculated at different temperatures and for different lengths. Short-range repulsive interactions between the monomers are assumed. The knots configurations are generated on a three-dimensional cubic lattice and sampled by means of the Wang-Landau algorithm and of the pivot method. The obtained results show that the topological effects play a key role for short-length polymers. Three temperature regimes of the growth rate of the internal energy of the system are distinguished., Comment: 7 pages, 12 figures, LaTeX + RevTeX. With respect to the first version, in the second version the text has been improved and all figures are now in black and white