Physical mechanism for biopolymers to aggregate and maintain in non-equilibrium states

Abstract

Many human or animal diseases are related to aggregation of proteins. A viable biological organism should maintain in non-equilibrium states. How protein aggregate and why biological organisms can maintain in non-equilibrium states are not well understood. As a first step to understand such complex systems problems, we consider simple model systems containing polymer chains and solvent particles. The strength of the spring to connect two neighboring monomers in a polymer chain is controlled by a parameter s with s → ∞ for rigid-bond. The strengths of bending and torsion angle dependent interactions are controlled by a parameter s A with s A → −∞ corresponding to no bending and torsion angle dependent interactions. We find that for very small s A, polymer chains tend to aggregate spontaneously and the trend is independent of the strength of spring. For strong springs, the speed distribution of monomers in the parallel (along the direction of the spring to connect two neighboring monomers) and perpendicular directions have different effective temperatures and such systems are in non-equilibrium states.

Universality and scaling in human and social systems

“…It is of interest to know whether the concepts and methods from critical physical systems can be useful for understanding complicated biological and human-social systems. In previous papers [35][36][37][38][39][40][41][42][43], we had pointed out that the ideas and methods of statistical physics can be useful for understanding some interesting biological problems. In this paper, I would like to point out that such methods and concepts can also be useful for understanding some interesting human and social systems.…”

Nematic and smectic liquid crystals modeling with stiff and free-joint Lennard-Jones chain molecules

“…On the basis of our previous works on molecular models of polymers [12][13][14][15][16], in this paper we will construct simple models of chain molecules which can show various phases of LCs. Our models can be extended to study the effects of nanoparticles or external fields on the structure of LCs.…”

“…For molecules with weak geometric anisotropy [23][24][25], the fluctuation of the reorientation of molecules prevents the system from having an orientation ordered configuration. In a system of stiff polymer chains, the molecules have a strong tendency to align with each other [14][15][16][26][27][28], as soon as the hindrance along the backbones of the molecules is sufficiently weak [14][15][16]. Under such a circumstance, the formation of stacks of plate like crystallites [27] on a substrate or that of bundles [14][15][16] in free space is guided by the backbone alignment.…”

“…In a system of stiff polymer chains, the molecules have a strong tendency to align with each other [14][15][16][26][27][28], as soon as the hindrance along the backbones of the molecules is sufficiently weak [14][15][16]. Under such a circumstance, the formation of stacks of plate like crystallites [27] on a substrate or that of bundles [14][15][16] in free space is guided by the backbone alignment. The clustering process proceeds in such a way that the alignment among molecules over local segments extends along the backbones, to reach a global extent [14][15][16].…”

“…Under such a circumstance, the formation of stacks of plate like crystallites [27] on a substrate or that of bundles [14][15][16] in free space is guided by the backbone alignment. The clustering process proceeds in such a way that the alignment among molecules over local segments extends along the backbones, to reach a global extent [14][15][16]. It occurs at a lower density and at a temperature within the liquid-vapor two-phase coexistence regime [16], in which the molecules have sufficient accessible volume for reorienting to facilitate the alignment.…”