اشترك بالحزمة الذهبية واحصل على وصول غير محدود شمرا أكاديميا
تسجيل مستخدم جديدConformational dynamics and internal friction in homo-polymer globules: equilibrium vs. non-equilibrium simulations
86
0
0.0
(
0
)
تأليف
Thomas R. Einert
اسأل ChatGPT حول البحث
ﻻ يوجد ملخص باللغة العربية
We study the conformational dynamics within homo-polymer globules by solvent-implicit Brownian dynamics simulations. A strong dependence of the internal chain dynamics on the Lennard-Jones cohesion strength {epsilon} and the globule size NG is observed. We find two distinct dynamical regimes: a liquid- like regime (for {epsilon} < {epsilon}s) with fast internal dynamics and a solid-like regime (for {epsilon} > {epsilon}s) with slow internal dynamics. The cohesion strength {epsilon}s of this freezing transition depends on NG. Equilibrium simulations, where we investigate the diffusional chain dynamics within the globule, are compared with non-equilibrium simulations, where we unfold the globule by pulling the chain ends with prescribed velocity (encompassing low enough velocities so that the linear-response, viscous regime is reached). From both simulation protocols we derive the internal viscosity within the globule. In the liquid-like regime the internal friction increases continuously with {epsilon} and scales extensive in NG. This suggests an internal friction scenario where the entire chain (or an extensive fraction thereof) takes part in conformational reorganization of the globular structure.
قيم البحث
اقرأ أيضاً
Colonies of bacterial cells endowed with a pili-based self-propulsion machinery represent an ideal model system for studying how active adhesion forces affect structure and dynamics of many-particle systems. As a novel computational tool, we describe
here a highly parallel molecular dynamics simulation package for modeling of textit{Neisseria gonorrhoeae} colonies. Simulations are employed to investigate growth of bacterial colonies and the dependence of the colony structure on cell-cell interactions. In agreement with experimental data, active pilus retraction is found to enhance local ordering. For mixed colonies consisting of different types of cell types, the simulations show a segregation of cell types depending on the pili-mediated interactions, as seen in experiments. Using a simulated experimental setup, we study the power-spectral density of colony-shape fluctuations and the associated fluctuation-response relation. The simulations predict a strong violation of the equilibrium fluctuation-response relation across the measurable frequency range. Lastly, we illustrate the essential role of active force generation for colony dynamics by showing that pilus-mediated activity drives the spreading of colonies on surfaces and the invasion of narrow channels.
Adsorption of polymers to surfaces is crucial for understanding many fundamental processes in nature. Recent experimental studies indicate that the adsorption dynamics is dominated by non-equilibrium effects. We investigate the adsorption of a single
polymer of length $N$ to a planar solid surface in the absence of hydrodynamic interactions. We find that for weak adsorption energies the adsorption time scales $ sim N^{(1+2 u)/(1+ u)}$, where $ u$ is the Flory exponent for the polymer. We argue that in this regime the single chain adsorption is closely related to a field-driven polymer translocation through narrow pores. Surprisingly, for high adsorption energies the adsorption time becomes longer, as it scales $sim N^{(1+ u)}$, which is explained by strong stretching of the unadsorbed part of the polymer close to the adsorbing surface. These two dynamic regimes are separated by an energy scale that is characterised by non-equilibrium contributions during the adsorption process.
We provide a non-equilibrium thermodynamic description of the life-cycle of a droplet based, chemically feasible, system of protocells. By coupling the protocells metabolic kinetics with its thermodynamics, we demonstrate how the system can be driven
out of equilibrium to ensure protocell growth and replication. This coupling allows us to derive the equations of evolution and to rigorously demonstrate how growth and replication life-cycle can be understood as a non-equilibrium thermodynamic cycle. The process does not appeal to genetic information or inheritance, and is based only on non-equilibrium physics considerations. Our non-equilibrium thermodynamic description of simple, yet realistic, processes of protocell growth and replication, represents an advance in our physical understanding of a central biological phenomenon both in connection to the origin of life and for modern biology.
Recent thermophoretic experiments on colloidal suspensions revived an old debate, namely whether the Soret effect is properly described by thermostatics, or necessarily requires non-equilibrium thermodynamics. Based on colloidal transport theory and
the entropy production of the related viscous flow, our analysis leads to the conclusion that the equilibrium approach may work for small ions, yet fails for colloidal particles and polymers. Regarding binary molecular mixtures, our results shed some doubt on the validity of thermostatic approaches that derive the Soret coefficient from equilibrium potentials.
A geometric approach to the friction phenomena is presented. It is based on the holographic view which has recently been popular in the theoretical physics community. We see the system in one-dimension-higher space. The heat-producing phenomena are m
ost widely treated by using the non-equilibrium statistical physics. We take 2 models of the earthquake. The dissipative systems are here formulated from the geometric standpoint. The statistical fluctuation is taken into account by using the (generalized) Feynmans path-integral.
سجل دخول لتتمكن من نشر تعليقات
التعليقات
جاري جلب التعليقات
سجل دخول لتتمكن من متابعة معايير البحث التي قمت باختيارها
