arXiv subjects

Nobu C. Shirai

Publications and source records attributed to Nobu C. Shirai.

7 recordsLinked to original sources

arXiv2026

Universal Negative Energetic Elasticity in Polymer Chains: Crossovers among Random, Self-Avoiding, and Neighbor-Avoiding Walks

Negative energetic elasticity in gels challenges the conventional understanding of gel elasticity; despite extensive research, a concise explanation remains elusive. In this study, we use the weakly self-avoiding walk (the Domb-Joyce model; DJ model) and interacting self-avoiding walk (ISAW) to investigate the emergence of negative energetic elasticity in polymer chains. Using exact enumeration, we show that both the DJ model and ISAW exhibit negative energetic elasticity, which is caused by effective soft-repulsive interactions between polymer segments. Moreover, we find that a universal scaling law for the internal energy of both models, with a common exponent of $7/4$, holds consistently across both random-walk-self-avoiding-walk and self-avoiding-walk-neighbor-avoiding-walk crossovers. These findings suggest that negative energetic elasticity is a fundamental and universal property of polymer networks and chains.

cond-mat.soft↗

arXiv2026

Unified origin of negative energetic elasticity in a lattice polymer chain: soft self-repulsion and bending stiffness

We study a single lattice polymer chain under a fixed end-to-end distance, incorporating both Domb--Joyce (DJ) soft-core self-repulsion between polymer segments and a local bending-energy cost. By decomposing the stiffness into energetic and entropic contributions, we survey the parameter space defined by the self-repulsion strength and bending-energy cost. We find that the energetic contribution to stiffness is negative across the entire explored range, whereas the entropic contribution remains positive. These results unify two previously independent mechanisms of negative energetic elasticity -- solvent-induced self-repulsion and bending stiffness -- and demonstrate that either mechanism alone, as well as their combination, produces the same sign. Beyond this sign-level unification, we analyze the internal-energy scaling and show that, in the absence of the bending-energy term, the DJ (self-repulsion) limit exhibits a robust $(n-r)^{7/4}/n$ scaling collapse. In contrast, the introduction of finite bending stiffness progressively disrupts this scaling, providing an internal-energy-based diagnostic to distinguish between contributions from self-repulsion and bending stiffness.

cond-mat.soft↗

arXiv2023

Solvent-Induced Negative Energetic Elasticity in a Lattice Polymer Chain

The negative internal energetic contribution to the elastic modulus (negative energetic elasticity) has been recently observed in polymer gels. This finding challenges the conventional notion that the elastic moduli of rubberlike materials are determined mainly by entropic elasticity. However, the microscopic origin of negative energetic elasticity has not yet been clarified. Here, we consider the $n$-step interacting self-avoiding walk on a cubic lattice as a model of a single polymer chain (a subchain of a network in a polymer gel) in a solvent. We theoretically demonstrate the emergence of negative energetic elasticity based on an exact enumeration up to $n=20$ and analytic expressions for arbitrary $n$ in special cases. Furthermore, we demonstrate that the negative energetic elasticity of this model originates from the attractive polymer--solvent interaction, which locally stiffens the chain and conversely softens the stiffness of the entire chain. This model qualitatively reproduces the temperature dependence of negative energetic elasticity observed in the polymer-gel experiments, indicating that the analysis of a single chain can explain the properties of negative energetic elasticity in polymer gels.

cond-mat.soft↗

arXiv2016

The interplay of intrinsic disorder and macromolecular crowding on α-synuclein fibril formation

α-synuclein (α-syn) is an intrinsically disordered protein which is considered to be one of the causes of Parkinson's disease. This protein forms amyloid fibrils when in a highly concentrated solution. The fibril formation of α-syn is induced not only by increases in α-syn concentration but also by macromolecular crowding. In order to investigate the coupled effect of the intrinsic disorder of α-syn and macromolecular crowding, we construct a lattice gas model of α-syn in contact with a crowding agent reservoir based on statistical mechanics. The main assumption is that α-syn can be expressed as coarse-grained particles with internal states coupled with effective volume; and disordered states are modeled by larger particles with larger internal entropy than other states. Thanks to the simplicity of the model, we can exactly calculate the number of conformations of crowding agents, and this enables us to prove that the original grand canonical ensemble with a crowding agent reservoir is mathematically equivalent to a canonical ensemble without crowding agents. In this expression, the effect of macromolecular crowding is absorbed in the internal entropy of disordered states; it is clearly shown that the crowding effect reduces the internal entropy. Based on Monte Carlo simulation, we provide scenarios of crowding-induced fibril formation. We also discuss the recent controversy over the existence of helically folded tetramers of α-syn, and suggest that macromolecular crowding is the key to resolving the controversy.

q-bio.BM↗

arXiv2013

Structural flexibility of intrinsically disordered proteins induces stepwise target recognition

An intrinsically disordered protein (IDP) lacks a stable three-dimensional structure, while it folds into a specific structure when it binds to a target molecule. In some IDP-target complexes, not all target binding surfaces are exposed on the outside, and intermediate states are observed in their binding processes. We consider that stepwise target recognition via intermediate states is a characteristic of IDP binding to targets with "hidden" binding sites. To investigate IDP binding to hidden target binding sites, we constructed an IDP lattice model based on the HP model. In our model, the IDP is modeled as a chain and the target is modeled as a highly coarse-grained object. We introduced motion and internal interactions to the target to hide its binding sites. In the case of unhidden binding sites, a two-state transition between the free states and a bound state is observed, and we consider that this represents coupled folding and binding. Introducing hidden binding sites, we found an intermediate bound state in which the IDP forms various structures to temporarily stabilize the complex. The intermediate state provides a scaffold for the IDP to access the hidden binding site. We call this process multiform binding. We conclude that structural flexibility of IDPs enables them to access hidden binding sites, and this is a functional advantage of IDPs.

q-bio.BM↗

arXiv2013

How to estimate the number of self-avoiding walks over 10^100? Use random walks

Counting the number of N-step self-avoiding walks (SAWs) on a lattice is one of the most difficult problems of enumerative combinatorics. Once we give up calculating the exact number of them, however, we have a chance to apply powerful computational methods of statistical mechanics to this problem. In this paper, we develop a statistical enumeration method for SAWs using the multicanonical Monte Carlo method. A key part of this method is to expand the configuration space of SAWs to random walks, the exact number of which is known. Using this method, we estimate a number of N-step SAWs on a square lattice, c_N, up to N=256. The value of c_256 is 5.6(1)*10^108 (the number in the parentheses is the statistical error of the last digit) and this is larger than one googol (10^100).

cond-mat.stat-mech↗

arXiv2013

Multicanonical simulation of the Domb-Joyce model and the Go model: new enumeration methods for self-avoiding walks

We develop statistical enumeration methods for self-avoiding walks using a powerful sampling technique called the multicanonical Monte Carlo method. Using these methods, we estimate the numbers of the two dimensional N-step self-avoiding walks up to N=256 with statistical errors. The developed methods are based on statistical mechanical models of paths which include self-avoiding walks. The criterion for selecting a suitable model for enumerating self-avoiding walks is whether or not the configuration space of the model includes a set for which the number of the elements can be exactly counted. We call this set a scale fixing set. We selected the following two models which satisfy the criterion: the Go model for lattice proteins and the Domb-Joyce model for generalized random walks. There is a contrast between these two models in the structures of the configuration space. The configuration space of the Go model is defined as the universal set of self-avoiding walks, and the set of the ground state conformation provides a scale fixing set. On the other hand, the configuration space of the Domb-Joyce model is defined as the universal set of random walks which can be used as a scale fixing set, and the set of the ground state conformation is the same as the universal set of self-avoiding walks. From the perspective of enumeration performance, we conclude that the Domb-Joyce model is the better of the two. The reason for the performance difference is partly explained by the existence of the first-order phase transition of the Go model.

cond-mat.stat-mech↗