A Note on Vestigial Osmotic Pressure.

Recent experiments have indicated that at least a part of the osmotic pressure across the giant unilamellar vesicle (GUV) membrane was balanced by the rapid formation of the monodisperse daughter vesicles inside the GUVs through an endocytosis-like process. Therefore, we investigated a possible osmotic role played by these daughter vesicles for the maintenance of osmotic regulation in the GUVs and, by extension, in living cells. We highlighted a mechanism whereby the daughter vesicles acted as osmotically active solutes (osmoticants), contributing an extra vestigial osmotic pressure component across the membrane of the parent vesicle, and we showed that the consequences were consistent with experimental observations.

Kinetic assays of DNA polymerase fidelity: A theoretical perspective beyond Michaelis-Menten kinetics.

The high fidelity of DNA polymerase (DNAP) is critical for the faithful replication of DNA. There are several quantitative approaches to measure DNAP fidelity. Directly counting the error frequency in the replication products gives the true fidelity but it turns out very hard to implement in practice.

Spontaneous Freezing of Water between 233 and 235 K Is Not Due to Homogeneous Nucleation.

The spontaneous freezing of microdroplets around 233 K has long been regarded as the occurrence of homogeneous ice nucleation. The corresponding temperature has been directly regarded as the homogeneous ice nucleation temperature, which is an intrinsic character of water. However, many recent investigations indicate that the spontaneous freezing may be still induced by surfaces of the water microdroplets or the residual impurities inside.

Template-specific fidelity of DNA replication with high-order neighbor effects: A first-passage approach.

DNA replication fidelity is a critical issue in molecular biology. Biochemical experiments have provided key insights on the mechanism of fidelity control by DNA polymerases in the past decades, whereas systematic theoretical studies on this issue began only recently. Because of the underlying difficulties of mathematical treatment, comprehensive surveys on the template-specific replication kinetics are still rare.

Behaviors of Glioblastoma Cells in in Vitro Microenvironments.

Glioblastoma (GBM) is the most malignant and highly aggressive brain tumor. In this study, four types of typical GBM cell lines (LN229, SNB19, U87, U251) were cultured in a microfabricated 3-D model to study their in vitro behaviors. The 3-D in vitro model provides hollow micro-chamber arrays containing a natural collagen interface and thus allows the GBM cells to grow in the 3-D chambers.

Proofreading of DNA polymerase: a new kinetic model with higher-order terminal effects.

The fidelity of DNA replication by DNA polymerase (DNAP) has long been an important issue in biology. While numerous experiments have revealed details of the molecular structure and working mechanism of DNAP which consists of both a polymerase site and an exonuclease (proofreading) site, there were quite a few theoretical studies on the fidelity issue. The first model which explicitly considered both sites was proposed in the 1970s and the basic idea was widely accepted by later models.

A general theory of kinetics and thermodynamics of steady-state copolymerization.

Kinetics of steady-state copolymerization has been investigated since the 1940s. Irreversible terminal and penultimate models were successfully applied to a number of comonomer systems, but failed for systems where depropagation is significant. Although a general mathematical treatment of the terminal model with depropagation was established in the 1980s, a penultimate model and higher-order terminal models with depropagation have not been systematically studied, since depropagation leads to hierarchically-coupled and unclosed kinetic equations which are hard to solve analytically.

Effect of side-chain length on structural and dynamic properties of ionic liquids with hydroxyl cationic tails.

The recent study has revealed that ionic liquids (ILs) with hydroxyl cationic tails are polar liquids without tightly aggregated nonpolar tail domains. Nevertheless, the influence of varying side-chain length on their microscopic structure and dynamics is still unclear. By performing all-atom molecular dynamics simulations for 1-(n-hydroxyalkyl)-3-methylimidazolium nitrate, where n varies from 2 to 12, we found that, with increasing side-chain length, both the nonpolar region and the flexibility of cationic tails increase.

Controlling the morphology of membranes by excess surface charge in cat-anionic fluorinated surfactant mixtures.

The segregation and phase sequence of semifluorinated cat-anionic surfactant membranes at different excess surface charges was investigated by freeze-fracture transmission electron microscope (FF-TEM), X-ray diffraction (XRD), and nuclear magnetic resonance (NMR). The thermal behavior of the membranes was evaluated by conductivity, rheology, and deuterium nuclear magnetic resonance ((2)H NMR). The experimental results show that the cat-anionic fluorinated surfactant mixtures can form faceted vesicles and punctured lamellar phase when there is excess surface charge.

Master equation approach for a cross-bridge power-stroke model with a finite number of motors.

The cross-bridge power-stroke model has been widely used to describe the motion of large motor assemblies connected to a common rigid filament. In this paper, we go beyond the original velocity-ensemble approach and propose a master equation approach to account for the cooperative motion of a finite number of motors based on the cross-bridge model. By studying the force-velocity relationship for motors with strain-independent detachment rate, we show the convergence of our approach to the velocity-ensemble approach in the limit of large motor numbers.

Concentration and temperature dependences of polyglutamine aggregation by multiscale coarse-graining molecular dynamics simulations.

The solvent-free multiscale coarse-graining model of polyglutamine was employed to study polyglutamine aggregation at different concentrations and temperatures by means of molecular dynamics simulation. The heterogeneity order parameter (HOP) was used to quantify the polyglutamine aggregation. Our simulation results demonstrate that polyglutamine aggregation is sensitive to concentration and temperature changes.

The neck linker of kinesin 1 seems optimally designed to approach the largest stepping velocity: a simulation study of an ideal model.

The neck linker is widely believed to play a critical role in the hand-over-hand walking of conventional kinesin 1. Experiments have shown that change of the neck linker length will significantly change the stepping velocity of the motor. In this paper, we studied this length effect based on a highly simplified chemically powered ratchet model.

FoF1-ATPase, rotary motor and biosensor.

F(o)F(1)-ATPase is an amazing molecular rotary motor at the nanoscale. Single molecule technologies have contributed much to the understanding of the motor. For example, fluorescence imaging and spectroscopy revealed the physical rotation of isolated F(1) and F(o), or F(o)F(1) holoenzyme.

Generalized integral fluctuation theorem for diffusion processes.

Using Feynman-Kac and Cameron-Martin-Girsanov formulas, we find a generalized integral fluctuation theorem (GIFT) for general diffusion processes by constructing a time-invariable integral. The existing integral fluctuation theorems can be derived as its specific cases. We interpret the origin of the GIFT in terms of time reversal of stochastic systems.

Temperature dependence of circular DNA topological states.

Circular double-stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo simulation, we predict the temperature dependence of the linking number distribution of small circular DNAs.

Shear-induced domain deformation in a tilted lipid monolayer: from circle to ellipse and kinked stripe.

The shear-induced domain deformation in a lipid monolayer comprised of tilted molecules is studied as a mechanical balance between surface pressure, line tension, electrostatic energy due to the dipole-dipole interaction, hexatic-elastic stress, and viscous stress. It is found that a simple shear can deform a circular domain into an elliptic shape with the long axis inclined 45 degrees from the shear direction. The "ellipse" is elongated in the long axis as shear rate increases, and evolves to a straight or kinked stripe, which was observed as a "shear band" by Fuller's group [Science 274, 233 (1996)] and "avalanche-like fronts" by Schwaltz's group [Langmuir 17, 3017 (2001)], at a threshold shear rate.

Bayesian analysis of folding and unfolding time series of single-forced RNAs.

On the basis of a coarse-grain physical model of the folding and unfolding of single-forced RNAs conducted in light tweezer experiments, we theoretically investigate the feasibility of inferring the RNA's intrinsic kinetic parameters from the noisy time series of the molecule's extension. A Bayesian approach using Monte Carlo Markov Chain is proposed. We prove that this statistical approach is efficient and accurate in inferring the molecule's physical parameters, even if the experimental data are yielded under a narrow range of forces.

Two-pathway four-state kinetic model of thioredoxin-catalyzed reduction of single forced disulfide bonds.

Recent single-molecule experiments found that the thioredoxin-catalyzed reduction of individual disulfide bonds placed under a stretching mechanical force has distinct characteristics: the reduction rate of human thioredoxin monotonically decreases with the force, while the rate of E. coli thioredoxin first decreases and then increases as the force goes beyond a certain threshold. In this work, we present a force-dependent two-pathway four-state model to uniformly quantify these intriguing observations.

Reversible transitions between peptide nanotubes and vesicle-like structures including theoretical modeling studies.

Peptide-based self-assembling systems are increasingly attractive because of their wide range of applications in different fields. Peptide nanostructures are flexible with changes in the ambient conditions. Herein, a reversible shape transition between self-assembled dipeptide nanotubes (DPNTs) and vesicle-like structures is observed upon a change in the peptide concentration.

A kinetic model of transcription initiation by RNA polymerase.

We establish a sequence-dependent kinetic model for the later stage of transcription initiation by RNA polymerase. We suggest that there are three reaction pathways, the abortive pathway, the scrunching pathway and the escape pathway, competitive with each other at each site during the transcription initiation. Using this three-pathway model, we mainly calculate the maximum sizes of the abortive transcripts, the abortive probabilities and the abortive/productive ratios for different promoters by Monte Carlo simulation and analytical methods.

Simulating the collapse transition of a two-dimensional semiflexible lattice polymer.

It has been revealed by mean-field theories and computer simulations that the nature of the collapse transition of a polymer is influenced by its bending stiffness epsilon(b). In two dimensions, a recent analytical work demonstrated that the collapse transition of a partially directed lattice polymer is always first order as long as epsilon(b) is positive [H. Zhou et al.

Force modulating dynamic disorder: a physical model of catch-slip bond transitions in receptor-ligand forced dissociation experiments.

Recent experiments found that some adhesive receptor-ligand complexes have counterintuitive catch-slip transition behaviors: the mean lifetimes of these complexes first increase (catch) with initial application of a small external force, and then decrease (slip) when the force is beyond some threshold. In this work we suggest that the forced dissociation of these complexes might be a typical rate process with dynamic disorder. The one-dimensional force modulating Agmon-Hopfield model is used to describe the transitions in the single-bond P-selectin glycoprotein ligand 1-P-selectin forced dissociation experiments, which were respectively performed in the constant force [Marshall, Nature (Landon) 423, 190 (2003)] and the ramping force [Evans, Proc.

Shape and stability of two-dimensional lipid domains with dipole-dipole interactions.

We study the general energy and shape of the two-dimensional solid monolayer domains with the dipole-dipole interactions. Compared with the domain energy without tilted dipole moments [M. Iwamoto and Z.

Collapse transition of two-dimensional flexible and semiflexible polymers.

The nature of the globule-coil transition of surface-confined polymers has been an issue of debate. Here this 2D collapse transition is studied through a partially directed lattice model. In the general case of polymers with positive bending stiffness (Delta>0), the collapse transition is first order; it becomes second order only in the limiting case of zero bending stiffness (Delta triple bond 0).

Single molecule Michaelis-Menten equation beyond quasistatic disorder.

The classic Michaelis-Menten equation describes the catalytic activities for ensembles of enzyme molecules very well. But recent single-molecule experiments showed that the waiting time distribution and other properties of single enzyme molecules were not consistent with the prediction based on the ensemble viewpoint. They have contributed to the slow conformational changes of a single enzyme in the catalytic processes.