By the so-called wormlike chain （WLC） model in polymer physics envision- ing an isotropic rod that is continuously flexible, the force-extension relations of semi- flexible polymer chains strongly constrained by various confinements are theoretically investigated, including a slab-like confinement where the polymer chains are sandwiched between two parallel impenetrable walls, and a capped nanochannel confinement with a circular or rectangular cross-section where the chains are bounded in three directions. The Brownian dynamics （BD） simulations based on the generalized bead-rod （GBR） model are performed to verify the theoretical predictions.
In this study, it is demonstrated that the motion of hinges in single protein molecules can be modeled as general fractional Langevin dynamics of harmonically bound particles driven by non-local Gaussian noise with a power-law correlation. This conclusion was justified by comparing the theoretical predictions of the proposed model to the existing molecular dynamics simulations performed on the M6I mutant of phage T4 lysozyme and E. coli ribonuclease H1.
This paper aims at developing a stochastic-elastic model of a soft elastic body adhering on a wavy surface via a patch of molecular bonds. The elastic deformation of the system is modeled by using continuum contact mechanics, while the stochastic behavior of adhesive bonds is modeled by using Bell＇s type of exponential bond association/dissociation rates. It is found that for sufficiently small adhesion patch size or stress concentration index, the adhesion strength is insensitive to the wavelength but decreases with the amplitude of surface undulation, and that for large adhesion patch size or stress concentration index, there exist optimal values of the surface wavelength and amplitude for maximum adhesion strength.
This study intends to investigate how the elasticity of a bacterial phage can affect the process of DNA packaging and ejection. For this purpose, we propose a unified continuum and statistical mechanics model by taking into account the effects of DNA bending deformation, electrostatic repulsion between DNA-DNA strands and elastic deformation of the phage capsid. Based on such a model, we derive the quantitative relations between packaging force, elasticity of capsid, DNA length remaining in the capsid, osmotic pressure and ejection time. The theoretically predicted results are found to agree very well with in vitro experimental observations in the lit-erature.
Receptor diffusion on cell membrane is usually believed as a major factor that controls how fast a virus can enter into host cell via endocytosis.However,when receptors are densely distributed around the binding site so that receptor recruiting through diffusion is no longer energetically favorable,we thus hypothesize that another effect,the creep deformation of cytoskeleton,might turn to play the dominant role in relaxing the engulfing process.In order to deeply understand this mechanism,we propose a viscoelastic model to investigate the dynamic process of virus engulfment retarded by the creep deformation of cytoskeleton and driven by the binding of ligand-receptor bonds after overcoming resistance from elastic deformation of lipid membrane and cytoskeleton.Based on this new model,we predict the lower bound of the ligand density and the range of virus size that allows the complete engulfment,and an optimal virus size corresponding to the smallest wrapping time.Surprisingly,these predictions can be reduced to the previous predictions based on simplified membrane models by taking into account statistical thermodynamic effects.The results presented in this study may be of interest to toxicologists,nanotechnologists,and virologists.
