On the Physics of Size Selectivity

We demonstrate that two mechanisms used by biological ion channels to select particles by size are driven by entropy. With uncharged particles in an infinite cylinder, we show that a channel that attracts particles is small-particle selective and that a channel that repels water from the wall is large-particle selective. Comparing against extensive density-functional theory calculations of our model, we find that the main physics can be understood with surprisingly simple bulk models that neglect the confining geometry of the channel completely.Comment: 4 pages, 3 figures, Phys. Rev. Lett. (accepted

Voltage sensing in ion channels: Mesoscale simulations of biological devices

Electrical signaling via voltage-gated ion channels depends upon the function of a voltage sensor (VS), identified with the S1-S4 domain in voltage-gated K+ channels. Here we investigate some energetic aspects of the sliding-helix model of the VS using simulations based on VS charges, linear dielectrics and whole-body motion. Model electrostatics in voltage-clamped boundary conditions are solved using a boundary element method. The statistical mechanical consequences of the electrostatic configurational energy are computed to gain insight into the sliding-helix mechanism and to predict experimentally measured ensemble properties such as gating charge displaced by an applied voltage. Those consequences and ensemble properties are investigated for two alternate S4 configurations, \alpha- and 3(10)-helical. Both forms of VS are found to have an inherent electrostatic stability. Maximal charge displacement is limited by geometry, specifically the range of movement where S4 charges and counter-charges overlap in the region of weak dielectric. Charge displacement responds more steeply to voltage in the \alpha-helical than the 3(10)-helical sensor. This difference is due to differences on the order of 0.1 eV in the landscapes of electrostatic energy. As a step toward integrating these VS models into a full-channel model, we include a hypothetical external load in the Hamiltonian of the system and analyze the energetic in/output relation of the VS.Comment: arXiv admin note: substantial text overlap with arXiv:1112.299

Optimal Algorithms for Train Shunting and Relaxed List Update Problems

This paper considers a Train Shunting problem which occurs in cargo train organizations: We have a locomotive travelling along a track segment and a collection of n cars, where each car has a source and a target. Whenever the train passes the source of a car, it needs to be added to the train, and on the target, the respective car needs to be removed. Any such operation at the end of the train incurs low shunting cost, but adding or removing truly in the interior requires a more complex shunting operation and thus yields high cost. The objective is to schedule the adding and removal of cars as to minimize the total cost. This problem can also be seen as a relaxed version of the well-known List Update problem, which may be of independent interest. We derive polynomial time algorithms for Train Shunting by reducing this problem to finding independent sets in bipartite graphs. This allows us to treat several variants of the problem in a generic way. Specifically, we obtain an algorithm with running time O(n^{5/2}) for the uniform case, where all low costs and all high costs are identical, respectively. Furthermore, for the non-uniform case we have running time of O(n^3). Both versions translate to a symmetric variant, where it is also allowed to add and remove cars at the front of the train at low cost. In addition, we formulate a dynamic program with running time O(n^4), which exploits the special structure of the graph. Although the running time is worse, it allows us to solve many extensions, e.g., prize-collection, economies of scale, and dependencies between consecutive stations

Shortest Path with Alternatives for Uniform Arrival Times: Algorithms and Experiments

The Shortest Path with Alternatives (SPA) policy differs from classical shortest path routing in the following way: instead of providing an exact list of means of transportation to follow, this policy gives such a list for each stop, and the traveler is supposed to pick the first option from this list when waiting at some stop. First, we show that an optimal policy of this type can be computed in polynomial time for uniform arrival times under reasonable assumptions. A similar result was so far only known for Poisson arrival times, which are less realistic for frequency-based public transportation systems. Second, we experimentally evaluate such policies. In this context, our main finding is that SPA policies are surprisingly competitive compared to traditional shortest paths, and moreover yield a significant reduction of waiting times, and therefore improvement of user experience, compared to similar greedy approaches. Specifically, for roughly 25% of considered cases, we could decrease the expected waiting time by at least 20%. To run our experiments, we also describe a tool-chain to derive the necessary information from the popular GTFS-format, therefore allowing the application of SPA policies to a wide range of public transportation systems

SRPT Is 1.86-competitive for Completion Time Scheduling

We consider the classical problem of scheduling preemptible jobs, that ar-rive over time, on identical parallel machines. The goal is to minimize the total completion time of the jobs. In standard scheduling notation of Graham et al. [5], this problem is denoted P | rj,pmtn | j cj. A pop-ular algorithm called SRPT, which always schedules the unfinished jobs with shortest remaining processing time, is known to be 2-competitive, see Phillips et al. [12, 13]. This is also the best known competitive ratio for any online algorithm. However, it is conjectured that the competitive ra-tio of SRPT is significantly less than 2. Even breaking the barrier of 2 is considered a significant step towards the final answer of this classical online problem. We improve on this open problem by showing that SRPT is 1.86-competitive. This result is obtained using the following method, which might be of general interest: We define two dependent random variables that sum up to the difference between the cost of an SRPT schedule and the cost of an optimal schedule. Then we bound the sum of the expected values of these random variables with respect to the cost of the optimal schedule, yielding the claimed competitiveness. Furthermore, we show a lower bound of 21/19 for SRPT, improving on the previously best known 12/11 due to Lu et al. [10]

Langevin Trajectories between Fixed Concentrations

We consider the trajectories of particles diffusing between two infinite baths of fixed concentrations connected by a channel, e.g. a protein channel of a biological membrane. The steady state influx and efflux of Langevin trajectories at the boundaries of a finite volume containing the channel and parts of the two baths is replicated by termination of outgoing trajectories and injection according to a residual phase space density. We present a simulation scheme that maintains averaged fixed concentrations without creating spurious boundary layers, consistent with the assumed physics

On the validity of modeling concepts for the simulation of groundwater flow in lowland peat areas – case study at the Zegveld experimental field

The groundwater flow models currently used in the western part of The Netherlands and in other similar peaty areas are thought to be a too simplified representation of the hydrological reality. One of the reasons is that, due to the schematization of the subsoil, its heterogeneity cannot be represented adequately. Moreover, the applicability of Darcy's law in these types of soils has been questioned, but this law forms the basis of most groundwater flow models. <br><br> With the purpose of assessing the typical heterogeneity of the subsoil and to verify the applicability of Darcy's law, geo-hydrological fieldwork was completed at an experimental field within a research area in the western part of The Netherlands. The assessments were carried out for the so-called Complex Confining Layer (CCL), which is the Holocene peaty to clayey layer overlying Pleistocene sandy deposits. Borehole drilling through the CCL with a hand auger was completed and revealed the typical heterogeneous character of this layer, showing a dominance of muddy, humified peat which is alternated with fresher peat and clay. <br><br> Slug tests were carried out to study the applicability of Darcy's law, given that previous studies suggested its non-validity for humified peat soils due to a variable horizontal hydraulic conductivity <i>K</i><sub>h</sub> with head differences. For higher humification degrees, the experiments indeed suggested a variable <i>K</i><sub>h</sub>, but this appeared to be the result of the inappropriate use of steady-state formulae for transient experiments in peaty environments. The muddy peat sampled has a rather plastic nature, and the high compressibility of this material leads to transient behavior. However, using transient formulae, the slug tests conducted for different initial groundwater heads showed that there was hardly any evidence of a variation of the hydraulic conductivity with the applied head differences. Therefore, Darcy's law can be used for typical peat soils present in The Netherlands. <br><br> The heterogeneity of the subsoil and the apparent applicability of Darcy's law were taken into account for the detailed heterogeneous model that was prepared for the research area. A MODFLOW model consisting of 13 layers in which 4 layers represent the heterogeneous CCL was set up for an average year, assuming steady-state conditions; and for the winter of 2009 to 2010, adopting transient conditions. The transient model was extended to simulate for longer periods with the objective of visualizing the flow paths through the CCL. The results from these models were compared with a 10 layer model, whereby the CCL is represented by a single layer assuming homogeneity. From the comparison of the two model types, the conclusion could be drawn that a single layer schematization of the CCL produces flowpath patterns which are not the same but still quite similar to a 4 layer representation of the CCL. However, the single layer schematization results in a considerable underestimation of the flow velocity, and subsequently a longer travel time, through the CCL. Therefore, a single layer model of the CCL seems quite appropriate to represent the general flow behavior of the shallow groundwater system, but would be inappropriate for transport modeling through the CCL

Scaling in Complex Systems: Analytical Theory of Charged Pores

In this paper we find an analytical solution of the equilibrium ion distribution for a toroidal model of a ionic channel, using the Perfect Screening Theorem (PST). The ions are charged hard spheres, and are treated using a variational Mean Spherical Approximation (VMSA) . Understanding ion channels is still a very open problem, because of the many exquisite tuning details of real life channels. It is clear that the electric field plays a major role in the channel behaviour, and for that reason there has been a lot of work on simple models that are able to provide workable theories. Recently a number of interesting papers have appeared that discuss models in which the effect of the geometry, excluded volume and non-linear behaviour is considered. We present here a 3D model of ionic channels which consists of a charged, deformable torus with a circular or elliptical cross section, which can be flat or vertical (close to a cylinder). Extensive comparisons to MC simulations were performed. The new solution opens new possibilities, such as studying flexible pores, and water phase transformations inside the pores using an approach similar to that used on flat crystal surfaces

Stochastic Route Planning in Public Transport

Journey planning is a key process in public transport, where travelers get informed how to make the best use of a given public transport system for their individual travel needs. A common trait of most available journey planners is that they assume deterministic travel times, but vehicles in public transport often deviate from their schedule. The present paper investigates the problem of finding journey plans in a stochastic environment. To fully exploit the flexibility inherent in multi-service public transport systems, we propose to use the concept of a routing policy instead of a linear journey plan. A policy is a state-dependent routing advice which specifies a set of services at each location from which the traveler is recommended to take the one that arrives first. We consider current time dependent policies, that is, when the routing advice at a given location is based solely on the current time. We propose two heuristic solutions that find routing policies that perform better than deterministic journey plans. A numerical comparison shows the achievable gains when applying the different heuristic policies based on extensive simulations on the public transport network of Budapest. The results show that the probability of arriving on time to a given destination can be significantly improved by following a policy instead of a linear travel plan