Cargo transportation by two species of motor protein

The cargo motion in living cells transported by two species of motor protein with different intrinsic directionality is discussed in this study. Similar to single motor movement, cargo steps forward and backward along microtubule stochastically. Recent experiments found that, cargo transportation by two motor species has a memory, it does not change its direction as frequently as expected, which means that its forward and backward step rates depends on its previous motion trajectory. By assuming cargo has only the least memory, i.e. its step direction depends only on the direction of its last step, two cases of cargo motion are detailed analyzed in this study: {\bf (I)} cargo motion under constant external load; and {\bf (II)} cargo motion in one fixed optical trap. Due to the existence of memory, for the first case, cargo can keep moving in the same direction for a long distance. For the second case, the cargo will oscillate in the trap. The oscillation period decreases and the oscillation amplitude increases with the motor forward step rates, but both of them decrease with the trap stiffness. The most likely location of cargo, where the probability of finding the oscillated cargo is maximum, may be the same as or may be different with the trap center, which depends on the step rates of the two motor species. Meanwhile, if motors are robust, i.e. their forward to backward step rate ratios are high, there may be two such most likely locations, located on the two sides of the trap center respectively. The probability of finding cargo in given location, the probability of cargo in forward/backward motion state, and various mean first passage times of cargo to give location or given state are also analyzed

Admissible pairs of Hermitian symmetric spaces in the perspective of the theory of varieties of minimal rational tangents

We study a pair (\mathcal{S}_0,\mathcal{S}) of irreducible Hermitian Symmetric Spaces of compact type (cHSS) in this paper, with the first aim being classifying all the admissible pairs (\mathcal{S}_0,\mathcal{S})). This notion is a natural generalization of the pairs of sub-diagram type originated by Jaehyun Hong and Ngaiming Mok ([HoM 10]). Based on this classification, we partially solve the rigidity problem for the admissible pairs (\mathcal{S}_0,\mathcal{S}) which was raised by Mok and Zhang (2014) ([MoZ 14]), culminating in determining a sufficient condition for the pairs being non-rigid and proving that special pairs, which show up in the classification procedure, are algebraic, as a weaker result than being rigid. However, whether special pairs are rigid or not remains unknown and needs further investigation in the framework of VMRT theory.Comment: 29 page

Comment on "Efficiency of Isothermal Molecular Machines at Maximum Power"

Comment on "Efficiency of Isothermal Molecular Machines at Maximum Power" (PRL 108, 210602 (2012), arXiv:1201.6396)Comment: So far, this manuscript has not been accepted for publication, and I do not want to work on it now. So I want to withdraw it

Comment on "Optimal Reaction Time for Surface-Mediated Diffusion"

In recent letter [Phys. Rev. Lett {\bf 105}, 150606 (2010)], the surface-mediated diffusion problem is theoretically discussed, and interesting results have been obtained. However, for more general cases, the ansatz of solutions of the diffusion equation, which is the starting point of their analysis, might not be appropriate. In this comment, suggested ansatz and corresponding methods will be presented.Comment: So far, this manuscription has not been accepted for publication, and I do not want to work on this topic no

A weaker rigidity theorem for pairs of hyperquadrics and its application

In this short article, we establish a rigidity theorem for pairs of hyperquadrics in a weaker sense, i.e., we impose a condition that minimal rational curves are preserved, which is stronger than inheriting a sub-VMRT structure, a notion raised by Mok & Zhang (2014). This problem has its source in a theorem of Tsai (1993), and the main result of this article can be applied back to give a more intrinsic proof of Tsai's theorem.Comment: 9 page

Shock of three-state model for intracellular transport of kinesin KIF1A

Recently, a three-state model is presented to describe the intracellular traffic of unconventional (single-headed) kinesin KIF1A [Phys. Rev. Lett. {\bf 95}, 118101 (2005)], in which each motor can bind strongly or weakly to its microtubule track, and each binding site of the track might be empty or occupied by one motor. As the usual two-state model, i.e. the totally asymmetric simple exclusion process (TASEP) with motor detachment and attachment, in steady state of the system, this three-state model also exhibits shock (or domain wall separating the high-density and low density phases) and boundary layers. In this study, using mean-field analysis, the conditions of existence of shock and boundary layers are obtained theoretically. Combined with numerical calculations, the properties of shock are also studied. This study will be helpful to understand the biophysical properties of the collective transport of kinesin KIF1A

Optimization of stochastic thermodynamic machines

The study of stochastic thermodynamic machines is one of the main topics in nonequilibrium thermodynamics. In this study, within the framework of Fokker-Planck equation, and using the method of characteristics of partial differential equation as well as the variational method, performance of stochastic thermodynamic machines is optimized according to the external potential, with the irreversible work $W_{irr}$, or the total entropy production $\Delta S_{\rm tot}$ equivalently, reaching its lower bound. Properties of the optimal thermodynamic machines are discussed, with explicit expressions of upper bounds of work output $W$, power $P$, and energy efficiency $\eta$ are presented. To illustrate the results obtained, typical examples with optimal protocols (external potentials) are also presented

Properties of sodium-driven bacterial flagellar motor: A two-state model approach

Bacterial flagellar motor (BFM) is one of the ion-driven molecular machines, which drives the rotation of flagellar filaments and enable bacteria to swim in viscous solutions. Understanding its mechanism is one challenge in biophysics. Based on previous models and inspired by the idea used in description of motor proteins, in this study one two-state model is provided. Meanwhile, according to corresponding experimental data, mathematical relationship between BFM membrane voltage and pH value of the environment, and relationship between internal and external sodium concentrations are given. Therefore, with model parameter values obtained by fitting theoretical results of torque-speed relation to recent experimental data, many biophysical properties of bacterial flagellar motor can be obtained for any pH values and any external sodium concentrations. Including the rotation speed, stall torque (i.e. the torque generated by BFM), rotation dispersion, and rotation randomness. In this study, the single-stator BFM will be firstly analyzed, and then properties of multiple-stator BFM are addressed briefly

Totally asymmetric simple exclusion process with one or two shortcuts

In this paper, the operation of totally asymmetric simple exclusion process with one or two shortcuts under open boundary conditions is discussed. Using both mathematical analysis and numerical simulations, we have found that, according to the method chosen by the particle at the bifurcation, the model can be separated into two different situations which lead to different results. The results obtained in this paper would be very useful in the road building, especially at the bifurcation of the road

Theoretical model of transcription based on torsional mechanics of DNA template

Transcription is the first step of gene expression, in which a particular segment of DNA is copied to RNA by the enzyme RNA polymerase (RNAP). Despite many details of the complex interactions between DNA and RNA synthesis disclosed experimentally, much of physical behavior of transcription remains largely unknown. Understanding torsional mechanics of DNA and RNAP together with its nascent RNA and RNA-bound proteins in transcription maybe the first step towards deciphering the mechanism of gene expression. In this study, based on the balance between viscous drag on RNA synthesis and torque resulted from untranscribed supercoiled DNA template, a simple model is presented to describe mechanical properties of transcription. With this model, the rotation and supercoiling density of the untranscribed DNA template are discussed in detail. Two particular cases of transcription are considered, transcription with constant velocity and transcription with torque dependent velocity. Our results show that, during the initial stage of transcription, rotation originated from the transcribed part of DNA template is mainly released by the rotation of RNAP synthesis. During the intermediate stage, the rotation is usually released by both the supercoiling of the untranscribed part of DNA template and the rotation of RNAP synthesis, with proportion depending on the friction coefficient in environment and the length of nascent RNA. However, with the approaching to the upper limit of twisting of the untranscribed DNA template, the rotation resulted from transcription will then be mainly released by the rotation of RNAP synthesis