Equivalence of two approaches for modeling ion permeation through a transmembrane channel with an internal binding site

Calculating tracer currents through narrow ion channels: beyond the independent particle model

Discrete state models of single-file ion permeation through a narrow ion channel pore are employed to analyze the ratio of forward to backward tracer current. Conditions under which the well-known Ussing formula for this ratio hold are explored in systems where ions do not move independently through the channel. Building detailed balance into the rate constants for the model in such a way that under equilibrium conditions (equal rate of forward versus backward permeation events) the Nernst equation is satisfied, it is found that in a model where only one ion can occupy the channel at a time, the Ussing formula is always obeyed for any number of binding sites, reservoir concentrations of the ions and electric potential difference across the membrane which the ion channel spans, independent of the internal details of the permeation pathway. However, numerical analysis demonstrates that when multiple ions can occupy the channel at once, the nonequilibrium forward/backward tracer flux ratio deviates from the prediction of the Ussing model. Assuming an appropriate effective potential experienced by ions in the channel, we provide explicit formulae for the rate constants in these models.

Thermal transport and thermoelectric properties of beta-graphyne nanostructures

Graphyne, an allotrope of graphene, is currently a hot topic in the carbon-based nanomaterials research community. Taking beta-graphyne as an example, we performed a comprehensive study of thermal transport and related thermoelectric properties by means of nonequilibrium Green's function (NEGF). Our simulation demonstrated that thermal conductance of beta-graphyne is only approximately 26% of that of the graphene counterpart and also shows evident anisotropy. Meanwhile, thermal conductance of armchair beta-graphyne nanoribbons (A-BGYNRs) presents abnormal stepwise width dependence. As for the thermoelectric property, we found that zigzag beta-graphyne nanoribbons (Z-BGYNRs) possess superior thermoelectric performance with figure of merit value achieving 0.5 at room temperature, as compared with graphene nanoribbons (~0.05). Aiming at obtaining a better thermoelectric coefficient, we also investigated Z-BGYNRs with geometric modulations. The results show that the thermoelectric performance can be enhanced dramatically (figure of merit exceeding 1.5 at room temperature), and such enhancement strongly depends on the width of the nanoribbons and location and quantity of geometric modulation. Our findings shed light on transport properties of beta-graphyne as high efficiency thermoelectrics. We anticipate that our simulation results could offer useful guidance for the design and fabrication of future thermoelectric devices.

Theoretical frameworks for multiscale modeling and simulation

Biomolecular systems have been modeled at a variety of scales, ranging from explicit treatment of electrons and nuclei to continuum description of bulk deformation or velocity. Many challenges of interfacing between scales have been overcome. Multiple models at different scales have been used to study the same system or calculate the same property (e.g., channel conductance). Accurate modeling of biochemical processes under in vivo conditions and the bridging of molecular and subcellular scales will likely soon become reality.